Screening method for identifying genes involved in plant cell cycle

ABSTRACT

The present invention relates to a method for screening proteins related to and/or involved in plant cell cycle. It further relates to proteins isolated with the method and the use of those proteins and/or the genes encoding those proteins for modulating plant yield and plant growth.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This is a national phase entry under 35 U.S.C. §371 of International Patent Application PCT/EP2009/066856, filed Dec. 10, 2009, published in English as International Patent Publication WO 2010/066849 A1 on Jun. 17, 2010, which claims the benefit under Article 8 of the Patent Cooperation Treaty to European Patent Application Serial No. 08171187.1, filed Dec. 10, 2008.

TECHNICAL FIELD

The present invention relates to a novel method for screening proteins related to and/or involved in plant cell cycles. It further relates to proteins isolated with the method and the use of those proteins and/or the genes encoding those proteins for modulating plant yield and plant growth.

BACKGROUND

Knowledge of the basic cell cycle machinery is a prerequisite to grasp how signaling pathways impinge on and regulate cell proliferation during plant growth and development in a changing environment. The fundamental underlying mechanisms of cell division are conserved among all eukaryotes, however, due to their sessile lifestyle, plants have evolved unique features. Plant genome sequence analysis revealed the existence of an unexpected high number of genes involved in cell proliferation (Capron et al., 2003; Vandepoele et al., 2002; Menges et al., 2005; Schultz et al., 2007), compared to other organisms. Microarray analysis showed that a lot of these follow a cell cycle-dependent expression profile (Menges et al., 2005), sustaining their role in cell cycle regulation.

SUMMARY OF THE INVENTION

To elucidate which molecular machines are involved in plant cell division, we isolated cellular complexes by TAP from Arabidopsis thaliana cell suspension cultures (Van Leene et al., 2007; Van Leene et al., 2008) using “core” cell cycle proteins as baits. The dataset was corrected for non-specific interactions and divided in a “core” dataset of interactions that were biologically confirmed in at least two independent repeats, and a “non-core” dataset. Surprisingly, we found that the datasets, apart from known cell cycle proteins, were also comprising proteins of which the role in cell cycle never has been illustrated before.

The robustness of both the core and non-core datasets is demonstrated through different computational analysis and through the biological interpretation of the network. The interactome serves as an excellent hypothesis-generating tool, and the power of it is reached in particular when integrated with other data. Combining our interactome data with cell cycle-related expression profiles, for example, gives insight in which CDK/cyclin complexes are active during cell division and when. The data prove that the high numbers of cell cycle regulators in plants are not the sole consequence of redundancy, but that different cell cycle regulators are combined in complexes providing functional diversity leading to increased complexity and flexibility of the plant cell cycle.

Disclosed herein is a method to isolate novel cell cycle-related proteins, comprising (1) performing a tap analysis using a known cell cycle protein as bait, (2) correcting the results for non-specific interactions, and (3) reconfirming the corrected results. “Reconfirming the result,” as used here, can be done either by repeating the tap-tag experiment or by carrying out a reversed tap-tag, wherein the original prey is now used as bait.

Also disclosed herein is the use of a cell cycle-related protein isolated with the method of the invention for the modulation of plant growth and/or yield. In a particular embodiment, the plant is a crop plant, preferably a monocot or a cereal, even more preferably it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.

The use, as indicated here, is the use of the protein and/or the use of a nucleic acid encoding this protein, or the complement thereof It includes, but is not limited to, genomic DNA, cDNA, messenger RNA (including the 5′ and 3′ untranslated regions) and RNAi; the use can result, as a non-limiting example, in overexpression or repression of the expression of the gene. Overexpression or repression of expression of a target gene can be obtained by transfer of a genetic construct, intended for the overexpression or the repression of expression into a plant. The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is a fairly routine technique known to the person skilled in the art. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include, but are not limited to, agrobacterium-mediated transformation, the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection.

Preferably, the cell cycle-related proteins are selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790, At4g38900, At3g49240, At5g24690, At1g06070, At4g34150, At1g20480, At5g20920, At3g15970, At5g13030, At1g01880, At5g07310, At2g46610, At1g10690, At3g04710, At3g24690, At4g16130, At2g05830, At1g29220, At1g55890, At1g60650, At1g70830, At2g43140, At1g77180, At5g18620, At5g02530, At5g14170, At1g52730, At2g33340, At1g03060, At3g62240, At4g38740, At5g61220, At3g53880, At3g56860, At1g01970, At1g19520, At1g14620, At2g03820, At3g01280, At3g56690, At5g41190, At5g03740, At1g42440, At2g28450, At1g09760, At1g10840, At3g11830, At5g54900, At1g31760, At1g61870, At3g11760, At1g05805, At1g29200, At4g13850, At4g38780, At1g71380, At3g13640, At5g25060, At1g43700, At2g46020, At3g55760 and At5g21160 or a variant thereof. “Variants,” as used here, are including, but not limited to, homologues, orthologues and paralogues of the cell cycle-related proteins. “Homologues” of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organisms that have originated through speciation, and are also derived from a common ancestral gene. Preferably, the homologue, orthologue or paralogue has a sequence identity at a protein level of at least 50%, 51%, 52%, 53%, 54% or 55%, 56%, 57%, 58%, 59%, preferably 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, more preferably 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, even more preferably 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and most preferably 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more as measured in a BLASTp (Altschul et al., 1997; Altschul et al., 2005).

Preferably, the use is overexpression of the gene encoding the cell cycle-related protein, even more preferably it is overexpression of a cell cycle-related protein according to the invention, selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790 (SEQ ID NOS:1-5), or a variant thereof. Preferably, overexpression results in an increase of plant growth and/or yield. Increase of plant growth and/or yield is measured by comparing the test plant, comprising a gene used according to the invention, with the parental, non-transformed plant, grown under the same conditions as control. Preferably, increase of growth is measured as an increase of biomass production. “Yield” refers to a situation where only a part of the plant, preferably an economically important part of the plant, such as the leaves, roots or seeds, is increased in biomass. The term “increase” as used here means at least a 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein. “Increase of plant growth,” as used here, is preferably measured as increase of any one or more of total plant biomass, leaf biomass, root biomass and seed biomass. In one preferred embodiment, the increase is an increase in total plant biomass. In a preferred embodiment, the plant is a crop plant, preferably a monocot or a cereal; even more preferably, it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.

Still another aspect of the invention is a novel cell cycle-related protein, isolated with the method according to the invention.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: Panel A: Enrichment analysis on the core and non-core datasets. Statistically significant enrichments are indicated with * (p-value<0.05) or with ** (p-value<0.01). An enrichment analysis was performed for genes showing cell cycle-regulated expression (Periodic), for genes containing an E2F or MSA consensus motif in their promoter and for proteins containing a CDK consensus phosphorylation site. Panel B: Percentage of the whole gene pool (genome-wide), a cell cycle collection of 518 genes, bait proteins (without reverse baits), and core and non-core preys (without the cell cycle collection) having at least two features. P-values are shown in red. Panel C: Distribution of the transcript PCC of the core (red curve) and non-core dataset (green curve), compared to the average distribution (black and grey curves) of 100 random networks containing an equal number of interactions and genes.

FIG. 2: Distribution of the number of cell cycle-related features among the whole gene pool (genome-wide), a collection of 518 cell cycle genes, and bait proteins (without reverse baits).

FIG. 3: Overview of the subnetworks.

FIG. 4: Fresh weight of control lines transformed with empty vector. About 100 plants were analyzed for each independent line (C1 and C2).

FIG. 5: Distribution of plants in function of their fresh weight. The graphs represent the frequency of a plant belonging to a certain category of weight.

FIG. 6: Distribution of plants in function of their fresh weight. The graphs represent the frequency of a plant belonging to a certain category of weight (% of plants versus fresh weight category, as in FIG. 5). The lines analyzed are independent lines of the ones presented in FIG. 5.

DETAILED DESCRIPTION OF THE INVENTION EXAMPLES MATERIALS AND METHODS TO THE EXAMPLES Cloning and TAP Purification

Cloning of transgenes encoding tag fusions under control of the constitutive Cauliflower tobacco mosaic virus 35S promoter, transformation of Arabidopsis cell suspension cultures, protein extract preparation, TAP purification, protein precipitation and separation were done as previously described (Van Leene et al., 2007). The adapted protocol used for purification of protein complexes incorporating GS-tagged bait is described elsewhere (Van Leen et al., 2008). For identification by mass spectrometry, minor adjustments were implemented compared to previously described protocols (Van Leene et al., 2007), as described below.

Proteolysis and Peptide Isolation

After destaining, gel slabs were washed for 1 hour in H₂O, polypeptide disulfide bridges were reduced for 40 minutes in 25 mL of 6.66 mM DTT in 50 mM NH₄HCO₃ and, sequentially, the thiol groups were alkylated for 30 minutes in 25 mL 55 mM IAM in 50 mM NH₄HCO₃. After washing the gel slabs three times with water, complete lanes from the protein gels were cut into slices, collected in microtiter plates and treated essentially as described before with minor modifications (Van Leene et al., 2007). Per microtiter plate well, dehydrated gel particles were rehydrated in 20 μL digest buffer containing 250 ng trypsin (MS Gold; Promega, Madison, Wis.), 50 mM NH₄HCO₃ and 10% CH₃CN (v/v) for 30 minutes at 4° C. After adding 10 μL of a buffer containing 50 mM NH₄HCO₃ and 10% CH₃CN (v/v), proteins were digested at 37° C. for 3 hours. The resulting peptides were concentrated and desalted with microcolumn solid phase tips (PerfectPure™ C18 tip, 200 nL bed volume; Eppendorf, Hamburg, Germany) and eluted directly onto a MALDI target plate (Opti-TOFTM384 Well Insert; Applied Biosystems, Foster City, Calif.) using 1.2 μL of 50% CH₃CN:0.1% CF₃COOH solution saturated with α-cyano-4-hydroxycinnamic acid and spiked with 20 fmole/μL Glu1 Fibrinopeptide B (Sigma Aldrich), 20 fmole/μL des-Pro2-Bradykinin (Sigma Aldrich), and 20 fmole/μL Adrenocorticotropic Hormone Fragment 18-39 human (Sigma Aldrich).

Acquisition of Mass Spectra

A MALDI tandem MS instrument (4700 and 4800 Proteomics Analyzer; Applied Biosystems) was used to acquire peptide mass fingerprints and subsequent 1 kV CID fragmentation spectra of selected peptides. Peptide mass spectra and peptide sequence spectra were obtained using the settings essentially as previously presented (Van Leene et al., 2007). Each MALDI plate was calibrated according to the manufacturers' specifications. All peptide mass fingerprinting (PMF) spectra were internally calibrated with three internal standards at m/z 963.516 (des-Pro2-Bradykinin), m/z 1570.677 (Glu1-Fibrinopeptide B), and m/z 2465,198 (Adrenocorticotropic Hormone Fragment 18-39) resulting in an average mass accuracy of 5 ppm±10 ppm for each analyzed peptide spot on the analyzed MALDI targets. Using the individual PMF spectra, up to sixteen peptides, exceeding a signal-to-noise ratio of 20 that passed through a mass exclusion filter, were submitted to fragmentation analysis.

MS-Based Protein Homology Identification

PMF spectra and the peptide sequence spectra of each sample were processed using the accompanied software suite (GPS Explorer 3.6, Applied Biosystems) with parameter settings essentially as previously described (Van Leene et al, 2007). Data search files were generated and submitted for protein homology identification by using a local database search engine (Mascot 2.1, Matrix Science). An in-house non-redundant Arabidopsis protein database called SNAPS Arabidopsis thaliana version 0.4 (SNAPS=Simple Non-redundant Assembly of Protein Sequences, 77488 sequence entries, 30468560 residues; available at WorldWideWeb.ptools.ua.ac.be/snaps) was compiled from nine public databases. Protein homology identifications of the top hit (first rank) with a relative score exceeding 95% probability were retained. Additional positive identifications (second rank and more) were retained when the score exceeded the 98% probability threshold. Because identifications were done with different versions of the SNAPS database (Van Leen et al., 2007), and with the goal to obtain more uniformity between the identifications, all identifications from the core and the non-core dataset were resubmitted to Mascot and identified with the protein sequence repertoire from the latest TAIR database (TAIR8.0). Furthermore, an additional restriction was implemented to reduce the number of false positive identifications and, as so, identifications for which more than 50% of the corresponding peptides had a trypsin miss-cleavage, were discarded.

GO Enrichment Analysis

Analysis of over- and under-representation of GO terms was done with the BiNGO tool (Maere et al., 2005) in Cytoscape (Shannon et al., 2003). The hypergeometric test was chosen at a significance value of 0.05 with the Benjamini and Hochberg False Discovery Rate Correction for multiple testing. The Arabidopsis gene annotation file used in the analysis was downloaded from the gene ontology website on the 4th of October 2008.

Cell Cycle Enrichment Analysis

For the periodic gene enrichment analysis, a list of 1258 genes showing cell cycle-regulated and cell cycle-associated expression was compiled from two datasets (Menges et al., 2003; Jensen et al., 2006). Genome wide corresponds to all 23834 genes present on the Affymtetrix ATH1 microarray. Genes containing E2F or M-specific activator (MSA) motifs in their promoter sequence were in silico determined by combining transcript expression data and comparative genomics (Vandepoele et al, 2006). Here, genome wide corresponds to 19173 genes for which a unique probe set is available on the ATH1 microarray. Proteins containing the CDK consensus phosphorylation site [ST]PX[KR], a known hallmark of CDK substrates (De Veylder et al., 1997), were considered as potential CDK substrates. The presence of the consensus motif was screened with the patmatch tool available at TAIR and, hence, genome wide corresponds here to all 27235 proteins present in the TAIR8.0 release. For all enrichment analysis, p-values were calculated with the hypergeometric cumulative distribution function of the Matlab 7.5 software. Proteins that could not be assigned to a specific gene locus were discarded from all enrichment analysis.

Overlap with Protein-Protein Databases

To assess the novelty of the cell cycle interactome, we screened for the overlap of our datasets with the following databases containing protein-protein interactions: TAIR (Huala et al., 2001), InTact (Kerrien et al., 2007), Arabidopsis Reactome (Tsesmetzis et al., 2008), AtPID (Cui et al., 2008), Reactome (Vastrik et al., 2007) and The Bio-Array Resource (BAR) for Arabidopsis Functional Genomics (Geisler-Lee et al., 2007).

Co-Expression Analysis

Transcript Pearson Correlation Coefficients (PCC), representing the degree of co-expression of gene pairs, were calculated based on an Arabidopsis ATH1 micro-array compendium of 518 experiments focused towards cell cycle or plant growth and development (Table 7). We compared the PCC distribution of both datasets with the PCC distribution of 100 randomized datasets with an equal number of randomly chosen proteins and interactions.

Constructs and Plant Transformation

The overexpressing constructs were produced by using gateway cloning technology. The cDNA of the genes of interest (table, sheet OE produced and LOF requested) were amplified by PCR from reverse transcribed RNA extracted from tissues of Arabidopsis thaliana ecotype Columbia. The PCR reactions were performed using the Phusion High fidelity DNA polymerase (Finnzymes) according to the manufacturer's instructions. The PCR fragments, corresponding to complete cDNA of the genes of interest were introduced into pDONr 201 using the Gateway system (Invitrogen) by attBXattP recombination sites and subsequently recombined into the pK7WG2 expression vector by attL XattR sites recombination. The sequence was confirmed by sequencing. The constructs containing the genes of interest under the control of the CaMV 35S promoter were used to transform Arabidopsis thaliana by the flowerdip method (Clough and Bent, 1998).

Plant Material and Growth Condition

Transgenic lines were identified by selection on MS medium (half-strength Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands), Sucrose 1%) supplemented with 50 mg/l kanamycin and later transferred to soil for seed production. A second selection on MS plus kanamycine allowed the selection of lines containing one site of insertion of the transgene. Plants were grown under a 16-hour day and 8-hour night regime at 21° C.

Biomass Test

For the biomass measurement, the vegetative part of a 20-day-old plant grown on MS medium was harvested and the fresh weight was measured by weighing about 60 plants of each line.

Example 1 Isolation of the TAP Complexes

As baits, we used 73 “core” cell cycle regulatory proteins (Vandepoele et al., 2002; Menges et al., 2006; Perez et al., 2007), four mitotic checkpoint proteins (Menges et al., 2005), eight anaphase promoting complex (APC) subunits and six APC activators (Capron et al., 2003), one 26S proteasome subunit (Brukhin et al., 2005), ten proteins involved in DNA replication or repair (Schultz et al., 2007), and as proof of concept, six proteins for reverse TAP experiments (Table 1). Of the 108 TAP fusions, 102 were expressed successfully. In total, 303 purifications were performed with at least two independent purifications per bait.

Example 2 Identification of the Prey Proteins

Purified proteins were identified via MALDI-TOFTOF. Non-specific proteins, determined by control purifications, were subtracted from the hit lists (Table 2), generating a non-redundant dataset of 857 interactions among 393 proteins. This dataset was divided in a “core” dataset of 371 interactions among 196 proteins, containing interactions that were biologically confirmed in at least two independent repeats or in the reciprocal experiment, and a “non-core” dataset with the remainder 486 interactions among 320 proteins.

Example 3 Enrichment Analysis

To assess the quality of the interactome, we performed different enrichment analysis on the core and non-core preys. In both datasets, the GO term “cell cycle” was highly enriched (Table 3). Additional GO enrichments demonstrate that cell cycle is linked to a myriad of biological processes including growth and development, response to stress and hormone stimuli, energy production, chromatin remodeling and others. Next, we observed an enrichment in the core dataset for genes periodically expressed during cell cycle (FIG. 1, Panel A). Furthermore, both datasets were enriched for genes with E2F or M-specific activator (MSA) motifs in their promoter. The less pronounced enrichments for the non-core dataset indicate that it is more biased for interactions linking the core cell cycle machinery with other pathways. This is supported by the fact that the non-core dataset is more enriched for potential CDK substrates, as assessed by the presence of CDK phosphorylation sites. The fact that these interactions were often not confirmed is likely due to the transient nature of, e.g., CDK/substrate interactions.

Example 4 Isolation of Novel Cell Cycle Genes

In a quest for new cell cycle-related proteins, we integrated different cell cycle-related features (Table 4). The distribution of the number of features per gene shows that a collection of known cell cycle genes (Table 5) is enriched for these features compared to the whole gene pool (FIG. 2). A clear shift between the whole gene pool and the cell cycle collection was visible at two features, as it was the case for the original bait list, validating the choice of our baits. In search for new cell cycle proteins, we started from the core and non-core prey list and subtracted the collection of known cell cycle genes. The percentage meeting the criterion of having at least two features is shown (FIG. 1, Panel B), and all classes are significantly enriched compared to the whole gene pool. By filtering for genes containing at least two features, we generated a list of 123 potential new cell cycle genes from the core and non-core dataset (Table 6).

The robustness of the data is further exemplified by the observation that 46% of the core and 8% of the non-core dataset interactions are between baits, as our baits are supposed to act in common pathways. Screening our data for overlap with existing protein-protein interaction databases learned that 66% of the core and 95% of the non-core dataset interactions are new. On the other hand, this implicates that one-third of the core dataset is validated by other means. Finally, interactions from both datasets tend to be more co-expressed compared to interactions from randomized datasets as assessed by calculation of the transcript Pearson Correlation Coefficient (PCC) (FIG. 1, Panel C). The integrated cell cycle interactome can be accessed through a Cytoscape webstart and is provided as a matrix pivot table that allows easy querying of the interactome. To demonstrate the biological importance of the interactome, a selection of subnetworks is discussed below, covering interactions from both the core and non-core dataset (FIG. 3).

Example 5 Isolated Genes of the CDK Complexes

Key players in cell cycle progression are cyclin-dependent kinase (CDK) complexes. CDKA;1, the Arabidopsis ortholog of yeast cdc2/cdc28, co-purified with all tested D-type cyclins and with A3-type cyclins, but not with the mitotic A1-, A2- or B-type cyclins. Combining our interactome data with expression data (Menges et al. 2005), we speculate that at cell cycle reentry and early in G1-phase, CDKA;1 binds CYCD3;3 and CYCD5;1. Further on in G1-phase and at the G1/S checkpoint, CDKA;1 binds a variety of D-type cyclins, such as CYCD4;1, CYCD4;2, CYCD3;1, CYCD6;1 and CYCD7;1. In addition, CDKA;1 interacts with S-phase specific A3-type cyclins. The other A- and B-type cyclins, of which most possess a peak of expression at the G2/M-boundary, bind the plant-specific mitotic B-type CDKs. B1-type cyclins associate exclusively with B2-type CDKs, while the remainder A- and B-type cyclins preferentially bind B1-type CDKs. Although transient interactions are more difficult to screen with TAP, our interactome contains different potential CDK substrates. As predicted (Geisler-Lee et al., 2007), CDKA;1 is present as a highly connected hub in the core network. It co-purified the unknown protein AT4G14310, which was further present in complexes with CKS1, CKS2, CYCA3;1, CyCA3;4 and KRP2 and the reverse purification confirmed interaction with CDKA;1 and CKS2 and revealed interaction with the plant-specific kinesin motor protein KCA2 involved in division plane determination. Next, CDKA;1 was pulled down with the 26S proteasome complex, purified through RPN1a, possibly reflecting cell cycle regulation of the 26S proteasome. CDKA;1 further interacted with three proteins from the UDP-xylose biosynthesis pathway, coupling cell cycle regulation with cell wall synthesis (Siefert, 2004). With three A-type cyclins, we picked up a DNA repair protein and with CYCB1;3, we found γ-tubulin and a spindle pole body component, two proteins involved in microtubule nucleation during, e.g., assembly of the preprophase band, a plant-specific structure required for polarity determination during cell cycle (Erhardt et al., 2002). Furthermore, some interesting chromatin-remodeling proteins were identified with different cyclins: CHR17, an E2F-up-regulated ISWI protein (Huanca-Mamani et al., 2005) interacted with CYCD3;2 and CYCD5;1. CHC1 associated with CYCA1;1, CYCD7;1, CYCB2;3 and CKS2, and BRAHMA, a SWI/SNF chromatin-remodeling ATPase implicated in the formation and/or maintenance of cotyledon boundary cells during embryogenesis (Kwon et al., 2006), was identified with CYCB1;3 and CYCB2;3.

Example 6 Isolation of Positive Regulators of the Cell Cycle

For full activity, CDKs require, next to cyclin binding, phosphorylation of a threonine residue within the T-loop by CDK-activating kinases (CAK). The Arabidopsis genome encodes four CAKs, namely, three D-type CDKs, homologous to human CDK7, and one cyclin-independent CAK-activating kinase (CAKAK) CDKF;1. Here, we show that both CDKD;2 and CDKD;3 form a trimeric complex with CYCH;1 and the CAK assembly factor MAT1. Like in rice (Rohila et al., 2006), CDKD;2 is also part of the basal TFIIH complex involved in transcription and DNA repair, as three members co-purified (UVH6/XPD, AT1G55750 and AT4G17020). In this complex, CDKD;2 activates transcription through phosphorylation of the C-Terminal Domain (CTD) of RNA polymerase II. With UVH6 and MAT1 as baits, we confirmed interaction with CDKD;2 and purified two more proteins of the TFIIH complex. CDKD;2 further co-purified proteins involved in nucleotide biosynthesis, namely, three ribose-phosphate pyrophosphokinases. More upstream, the monomeric CAKAK CDKF;1 activates CDKD;2 in a cyclin-independent manner. On the other hand, CDKF;1 also binds CDKG;2. The G-type CDK class has two members in Arabidopsis, and is homologous to the human cytokinesis-associated p58 galactosyltransferase protein. Here, we discovered CYCL1, a cyclin with a SR-like splicing domain (Forment et al., 2002), as the regulatory cyclin partner of both G-type CDKs, validating the clustering of CYCL1 with CDKG;2 in a tissue-specific gene expression analysis (Menges et al., 2005). Both core and non-core interacting proteins hint for a function of CDKG/CYCL complexes in regulation of transcription and splicing, so activation of CDKF;1 could lead to altered splicing events during cell proliferation.

Example 7 Isolation of Negative Regulators of the Cell Cycle

Negative regulation of cell cycle progression is achieved by docking of small proteins to the CDK/cyclin complexes. Arabidopsis encodes seven proteins related to the mammalian Kip/Cip inhibitors, known as Kip-related proteins (KRPs). Here, we show that all KRPs, except KRP1, interact with both CDKA;1 and D-type cyclins. With three KRPs, CDKB1;2 and two APC activators, we found an ethylene responsive AP2 transcription factor (TF), and with KRP2 we picked up a bZIP TF also found with B-type cyclins and CDKB1;2. In plants, a second family of cell cycle inhibitor proteins exist that are up-regulated by abiotic and biotic stress, comprising SIAMESE (SIM) and SIAMESE-Related (SMR) proteins (Peres et al., 2007; Churchman et al., 2006). SIM is a nuclear protein promoting endoreduplication in trichomes by suppression of mitosis. It was proposed that it inhibits mitosis through inhibition of CDKA;1/CYCD complexes (Churchman et al., 2006). In our dataset, however, SIM co-purifies CDKB1;1 and not CDKA;1, so endoreduplication may be triggered directly by inhibiting mitotic CDKB/cyclin complexes. Next to SIM, also SMR1 and SMR2 associate with CDKB1;1, and the CDKB1;1 interactor CYCB2;4 binds AT2G28330, an additional member of the SMR family. In contrast, SMR3-5 bind CDKA;1 and D-type cyclins. Besides, with CDKA;1 and different D-type cyclins as bait, we picked up two new members of the SMR clan, AT5G40460 and AT1G10690, and reverse purifications confirmed these interactions. As AT5G40460 was almost 20-fold induced in plants overexpressing E2Fa and DPa (Vandepoele et al., 2005), it may inhibit CDKA;1/CYCD complexes during S-phase preventing re-initiation of DNA replication. SMR1 further co-purified bZIP69, a TF also found with KRP3 and KRP5. Importins often co-purified both with KRPs and SMRs, supporting the importance of the regulation of their subcellular localization for their activity.

Example 8 Isolation of Genes Involved in Nucleotide Synthesis, DNA Replication and DNA Repair

At the G1/S boundary, CDKs activate the E2F/DP pathway by phosphorylation of the repressor RBR, inducing transcription of genes mainly involved in nucleotide synthesis, DNA replication and DNA repair. We demonstrate that E2Fa and E2Fb can associate both with DPa and DPb, and that all E2F and DP proteins co-purify RBR. Since CDKB1;1 interacted with DEL3, an atypical E2F protein lacking the trans-activation domain, we propose that DEL3 is regulated by CDKB1;1 activity, consistent with a second expression peak of DEL3 at G2/M (Menges et al., 2005). Interestingly, the mitotic CDKB1;1, and not CDKA;1, co-purified with RBR, providing further evidence that the E2F/DP/RBR network is not only active at G1/S but also at G2/M transitions, as was previously suggested in plants (Magyar et al., 2005) and mammalian cells (Ishida et al., 2001), or that mitotic CDK/cyclin complexes are active during S-phase as in yeast (Wuarin et al., 2002). We further identified some complexes involved in DNA replication, like the MCM complex, possessing helicase activity for unwinding of double-stranded DNA during DNA replication. This complex was isolated with MCM6 as bait, together with the recently published (Takahashi et al., 2008) and highly co-expressed E2F-target gene 1 (ETG1). The co-purified fraction of proliferating cell nuclear antigen 1 (PCNA1), a sliding clamp for DNA polymerase and thus a key actor in DNA replication, contained PCNA2, two DNA polymerase delta subunits (POLD1-2), of which one also interacted with CYCA2;3, an armadillo/beta-catenin repeat family of unknown function and a DNA binding protein. Furthermore, we prove the existence of the alternative Ctf18 replication factor C complex in plants, required for sister chromatid cohesion in yeast (Mayer et al., 2001) and a protein complex involved in stabilization of single-stranded DNA during replication, repair and transcription, including RPA2, two RPA3 proteins and a putative replication protein (Schultz et al., 2007).

Example 9 Analysis of Overexpression Lines

Thirty-two genes were cloned into expression vectors using Gateway cloning to produce plants overexpressing the genes of interest under the control of the CaMV35S promoter (table, sheet OE produced and LOF requested). These constructs were used for Arabidopsis thaliana transformation using the flower dip method. Primo-transformants were selected for all the constructs and grown for seed production. The seeds from eleven constructs (At5g25460, At3g01280, At1g31760, At3g21140, At3g17020, At1g05805, At1g10690, At1g56110, At5g24690, At5g60790, At1g09760) were harvested and used to select lines having one site of insertion of the transgene. A biomass test has been carried out on these segregating populations containing one insertion site. In this population, it is expected to find ¼ of wt, 2/4 of hemizygous and ¼ of homozygous plants. When the overexpression of a transgene leads to the production of larger plants, a fraction (¼ or ¾) of the plants analyzed will show an increased biomass. This method allows a fast screening of genes of which the overexpression gives a positive effect on plant growth. Plants were then grown under in vitro condition and the rosette fresh weight of approximately 60 plants was measured 20 days after stratification (table, sheet OE data+average). The control plants used in this experiment correspond to segregating plants transformed with an empty vector (C1 and C2). As shown in FIG. 4, for these two independent control lines, the plant fresh weight varies from 8 mg to 28 mg with an average of 20 mg. Among the eleven overexpressing lines analyzed, we found that for five (At1g56110, At3g17020, At3g21140, At5g25460, At5g60790), this distribution of weight is shifted towards larger plants than in the controls (FIG. 5). This shift in biomass range was found for three of these lines in two independent transformants (FIG. 6). The presence of larger plants in this segregating population proves that these five genes are involved in the control of growth.

TABLE 1 Overview of bait proteins used to elucidate the core cell cycle interactome of Arabidopsis thaliana. Topology = C- or N-terminal tag fusions. Tag refers to the applied tag being either the traditional TAP tag developed for Saccharomyces cerevisiae (15), or an optimized dual affinity tag (GS) (2). Expression was indicated as (+) if the TAP fusion protein could be detected by western blot analysis. The total number of purifications performed per bait is shown, with a minimum of two experiments. Bait Locus Category Topology Tag Expressed Purifications CDKA; 1 AT3G48750 core cell cycle C + N TAP + 11 CDKB1; 1 AT3G54180 core cell cycle C + N TAP + 4 CDKB1; 2 AT2G38620 core cell cycle C TAP + 2 CDKB2; 1 AT1G76540 core cell cycle N TAP + 2 CDKB2; 2 AT1G20930 core cell cycle C TAP + 4 CDKC; 1 AT5G10270 core cell cycle C TAP + 2 CDKC; 2 AT5G64960 core cell cycle C TAP + 4 CDKD; 1 AT1G73690 core cell cycle C TAP + 2 CDKD; 2 AT1G66750 core cell cycle C + N TAP + GS + 10 CDKD; 3 AT1G18040 core cell cycle C TAP + 2 CDKE; 1 AT5G63610 core cell cycle N TAP + 2 CDKF; 1 AT4G28980 core cell cycle C TAP + 3 CDKG; 1 AT5G63370 core cell cycle C GS + 2 CDKG; 2 AT1G67580 core cell cycle C TAP + 2 CKS1 AT2G27960 core cell cycle C TAP + GS + 10 CKS2 AT2G27970 core cell cycle C TAP + 2 CYCA1; 1 AT1G44110 core cell cycle C TAP + 2 CYCA1; 2 AT1G77390 core cell cycle C TAP − CYCA2; 1 AT5G25380 core cell cycle N TAP + 2 CYCA2; 2 AT5G11300 core cell cycle C TAP + 4 CYCA2; 3 AT1G15570 core cell cycle N TAP + 4 CYCA2; 4 AT1G80370 core cell cycle C TAP − CYCA3; 1 AT5G43080 core cell cycle C TAP + 4 CYCA3; 2 AT1G47210 core cell cycle N TAP − CYCA3; 3 AT1G47220 core cell cycle N GS + 2 CYCA3; 4 AT1G47230 core cell cycle C TAP + 4 CYCB1; 1 AT4G37490 core cell cycle C TAP + GS + 4 CYCB1; 2 AT5G06150 core cell cycle C TAP + 4 CYCB1; 3 AT3G11520 core cell cycle C TAP + 2 CYCB1; 4 AT2G26760 core cell cycle C TAP + 2 CYCB2; 1 AT2G17620 core cell cycle N TAP + 2 CYCB2; 2 AT4G35620 core cell cycle C TAP + 5 CYCB2; 3 AT1G20610 core cell cycle C TAP + 4 CYCB2; 4 AT1G76310 core cell cycle C GS + 2 CYCB2; 5 AT1G20590 core cell cycle C TAP + 2 CYCB3; 1 AT1G16330 core cell cycle N TAP + 4 CYCD1; 1 AT1G70210 core cell cycle C TAP − CYCD2; 1 AT2G22490 core cell cycle C TAP + 6 CYCD3; 1 AT4G34160 core cell cycle N TAP + 2 CYCD3; 2 AT5G67260 core cell cycle C TAP + 3 CYCD3; 3 AT3G50070 core cell cycle C TAP + 4 CYCD4; 1 AT5G65420 core cell cycle C TAP + 2 CYCD4; 2 AT5G10440 core cell cycle C TAP + 2 CYCD5; 1 AT4G37630 core cell cycle C TAP + 2 CYCD6; 1 AT4G03270 core cell cycle C TAP + 2 CYCD7; 1 AT5G02110 core cell cycle C GS + 2 CYCH; 1 AT5G27620 core cell cycle N TAP + 4 CYCT1; 3 AT1G27630 core cell cycle C TAP + 2 DEL1 AT3G48160 core cell cycle N TAP + 2 DEL2 AT5G14960 core cell cycle N TAP + 2 DEL3 AT3G01330 core cell cycle N TAP + 2 DPa AT5G02470 core cell cycle C TAP + 2 DPb AT5G03415 core cell cycle N TAP + 2 E2Fa AT2G36010 core cell cycle C TAP + GS + 5 E2Fb AT5G22220 core cell cycle N TAP + 2 E2Fc AT1G47870 core cell cycle C TAP + 5 KRP1 AT2G23430 core cell cycle N TAP + 2 KRP2 AT3G50630 core cell cycle N TAP + 6 KRP3 AT5G48820 core cell cycle N TAP + 4 KRP4 AT2G32710 core cell cycle N TAP + 6 KRP5 AT3G24810 core cell cycle N TAP + 2 KRP6 AT3G19150 core cell cycle N TAP + 4 KRP7 AT1G49620 core cell cycle N TAP + 2 RBR AT3G12280 core cell cycle N TAP + 2 WEE1 AT1G02970 core cell cycle N TAP + 4 Cdc25-like AT5G03455 core cell cycle C TAP + 2 MAT1 AT4G30820 core cell cycle N TAP + 2 SIM AT5G04470 core cell cycle C TAP + 4 SMR1 AT3G10525 core cell cycle C TAP + 4 SMR2 AT1G08180 core cell cycle C TAP + 2 SMR3 AT5G02420 core cell cycle C TAP + 2 SMR4 AT5G02220 core cell cycle C + N TAP + 4 SMR5 AT1G07500 core cell cycle N GS + 2 APC2 AT2G04660 APC core N TAP + 2 APC4 AT4G21530 APC core C TAP − APC7 AT2G39090 APC core N TAP + 2 APC8 AT3G48150 APC core N TAP + 2 APC10 AT2G18290 APC core N TAP + 4 APC11 AT3G05870 APC core C TAP + 2 CDC16 AT1G78770 APC core C TAP + 2 CDC27B AT2G20000 APC core C TAP + 2 CCS52A1 AT4G22910 APC activator N TAP + 4 CCS52A2 AT4G11920 APC activator N TAP + 6 CCS52B AT5G13840 APC activator N TAP + 4 CDC20.1 AT4G33270 APC activator N TAP + 2 CDC20.3 AT5G27080 APC activator N TAP + 2 CDC20.6 AT5G27945 APC activator C TAP − RPN1a AT2G20580 26S proteasome N TAP + 2 CDC6 AT2G29680 DNA replication N TAP + 2 CDC6b AT1G07270 DNA replication C TAP + 2 CTF8 AT5G52220 DNA replication N GS + 2 ETG1 AT2G40550 DNA replication C + N TAP + 4 MCM6 AT5G44635 DNA replication C TAP + 2 MCM7 AT4G02060 DNA replication C TAP + 2 ORC1a AT4G14700 DNA replication N TAP + 2 PCNA1 AT1G07370 DNA replication N TAP + 2 RPA2 AT2G24490 DNA replication N TAP + 2 UVH6 AT1G03190 DNA repair C TAP + 2 BUB3 AT1G69400 mitotic checkpoint N TAP + 2 BUB3-like AT3G19590 mitotic checkpoint N TAP + 2 BUBR1-like AT2G33560 mitotic checkpoint N TAP + 2 MAD2-like AT3G25980 mitotic checkpoint N TAP + 3 DL3195C AT4G14310 reverse N TAP + 2 F27G20.14 AT1G32310 reverse C GS + 2 expressed AT5G40460 reverse C TAP + 2 expressed AT1G10690 reverse N TAP + 2 UVI4 AT2G42260 reverse N TAP + 2 UVI4-like AT3G57860 reverse N TAP + 2

TABLE 2 List of control identifications. Control identifications determined by mock TAP (7) or GS (3) purifications, and by purifications with extracts from cultures expressing TAP fusions of heterologous GFP (7), RFP (2) or β-glucuronidase (5), or GS fusions of heterologous GFP (8), or β-glucuronidase (4). Ribosomal proteins, actins and tubulins identified in these control experiments were not included. The number of control experiments is shown between brackets. Accession number Protein name AT1G01460 phosphatidylinositol-4-phosphate 5-kinase family protein AT1G02400 gibberellin 2-oxidase, putative/GA2-oxidase, putative AT1G02500 S-adenosylmethionine synthetase 1 (SAM1) AT1G02930 glutathione S-transferase, putative AT1G04190 tetratricopeptide repeat (TPR)-containing protein AT1G04600 myosin, putative AT1G04690 potassium channel protein, putative AT1G05320 myosin-related AT1G05450 protease inhibitor/seed storage/lipid transfer protein (LTP)-related AT1G05970 expressed protein AT1G06220 elongation factor Tu family protein AT1G06780 glycosyl transferase family 8 protein AT1G07920 elongation factor 1-alpha AT1G07930 elongation factor 1-alpha AT1G08520 magnesium-chelatase subunit chlD, chloroplast, putative AT1G09080 luminal binding protein 3 (BiP-3) (BP3) AT1G09450 haspin-related AT1G09780 2,3-biphosphoglycerate-independent phosphoglycerate mutase, putative AT1G09980 expressed protein AT1G10270 pentatricopeptide (PPR) repeat-containing protein AT1G10390 nucleoporin family protein AT1G10590 DNA-binding protein-related AT1G11480 eukaryotic translation initiation factor-related AT1G12410 ATP-dependent Clp protease proteolytic subunit (ClpP2) AT1G13020 eukaryotic translation initiation factor, putative AT1G13440 glyceraldehyde 3-phosphate dehydrogenase, cytosolic, putative AT1G13610 expressed protein AT1G13910 F16A14.12 (leucine-rich repeat family protein) AT1G14315 Putative F-box protein AT1G14850 non-repetitive/WGA-negative nucleoporin family protein AT1G14980 10 kDa chaperonin (CPN10) AT1G15730 PRLI-interacting factor L, putative (Fragment) AT1G16030 heat shock protein 70, putative AT1G16410 cytochrome P450, putative AT1G16750 expressed protein AT1G18370 kinesin motor family protein (NACK1) AT1G19290 pentatricopeptide (PPR) repeat-containing protein AT1G19920 sulfate adenylyltransferase 2/ATP-sulfurylase 2 AT1G21480 exostosin family protein AT1G23410 ubiquitin extension protein, putative/40S ribosomal protein S27A AT1G24300 GYF domain-containing protein AT1G24510 T-complex protein 1 epsilon subunit, putative AT1G24938 hypothetical protein AT1G26750 expressed protein AT1G27430 GYF domain-containing protein AT1G27970 nuclear transport factor 2 (NTF2), putative AT1G29350 kinase-related AT1G29370 kinase-related AT1G31230 bifunctional aspartate kinase/homoserine dehydrogenase AT1G31280 PAZ domain-containing protein/piwi domain-containing protein (Fragment) AT1G31770 ABC transporter family protein AT1G34610 Ulp1 protease family protein AT1G35380 hypothetical protein AT1G36120 putative reverse transcriptase AT1G36280 adenylosuccinate lyase, putative/adenylosuccinase, putative AT1G36580 2,4-dienoyl-CoA reductase-related AT1G37200 gypsy-like retrotransposon family protein AT1G44900 DNA replication licensing factor, putative, similar to DNA replication licensing factor MCM2 AT1G48400 F-box family protein AT1G48630 guanine nucleotide-binding family protein/activated protein kinase AT1G49040 stomatal cytokinesis defective/SCD1 protein (SCD1) AT1G51380 eukaryotic translation initiation factor 4A, putative AT1G51710 ubiquitin-specific protease 6, putative (UBP6) AT1G52450 ubiquitin carboxyl-terminal hydrolase-related AT1G52740 histone H2A, putative AT1G53240 malate dehydrogenase [NAD], mitochondrial, putative AT1G53550 F-box family protein AT1G54270 eukaryotic translation initiation factor 4A-2 AT1G55490 RuBisCO subunit binding-protein beta subunit, chloroplast AT1G56070 elongation factor 2, putative AT1G56070 elongation factor 2, putative AT1G56410 heat shock cognate 70 kDa protein, putative AT1G58265 cytochrome P450-related AT1G59610 dynamin-like protein, putative (ADL3) AT1G61210 WD-40 repeat family protein/katanin p80 subunit, putative AT1G61300 disease resistance protein (NBS-LRR class), putative AT1G61570 mitochondrial import inner membrane translocase (TIM13) AT1G62020 coatomer protein complex, subunit alpha, putative AT1G62610 short-chain dehydrogenase/reductase (SDR) family protein AT1G62630 disease resistance protein (CC-NBS-LRR class), putative AT1G64520 26S proteasome regulatory subunit, putative (RPN12) AT1G64550 ABC transporter family protein AT1G65130 ubiquitin carboxyl-terminal hydrolase-related AT1G65290 acyl carrier family protein/ACP family protein AT1G65540 calcium-binding EF hand family protein AT1G65870 disease resistance-responsive family protein AT1G66410 calmodulin AT1G66510 AAR2 protein family AT1G67090 ribulose bisphosphate carboxylase small chain 1A AT1G68750 phosphoenolpyruvate carboxylase family protein AT1G68910 expressed protein similar to Myosin heavy chain, nonmuscle type B AT1G70100 expressed protein AT1G71220 UDP-glucose:glycoprotein glucosyltransferase, putative AT1G71270 Vps52/Sac2 family protein AT1G72000 beta-fructofuranosidase, putative/invertase, putative/ saccharase, putative AT1G72730 eukaryotic translation initiation factor 4A, putative AT1G73720 transducin family protein/WD-40 repeat family protein AT1G75010 MORN (Membrane Occupation and Recognition Nexus) repeat-containing protein AT1G76520 auxin efflux carrier family protein AT1G76530 auxin efflux carrier family protein AT1G77120 alcohol dehydrogenase (ADH) AT1G78130 transporter-related low similarity to spinster type III AT1G78390 9-cis-epoxycarotenoid dioxygenase, putative AT1G78900 vacuolar ATP synthase catalytic subunit A AT1G79280 expressed protein AT1G79550 phosphoglycerate kinase, putative AT1G79920 heat shock protein 70, putative AT1G79930 heat shock protein, putative AT1G80070 splicing factor, putative AT1G80270 DNA-binding protein, putative AT1G80670 transducin family protein/WD-40 repeat family protein AT2G01210 leucine-rich repeat transmembrane protein kinase, putative AT2G01350 quinolinate phosphoribosyl transferase family protein AT2G02160 zinc finger (CCCH-type) family protein AT2G03430 ankyrin repeat family protein AT2G04030 heat shock protein, putative AT2G05990 enoyl-[acyl-carrier protein] reductase [NADH], chloroplast, putative AT2G06850 xyloglucan:xyloglucosyl transferase AT2G07620 putative helicase AT2G07714 transcription factor-related similar to male sterility 1 proteins AT2G13680 callose synthase 5 (1,3-beta-glucan synthase) AT2G14120 dynamin-like protein 2b AT2G14880 SWIB complex BAF60b domain-containing protein AT2G16600 peptidyl-prolyl cis-trans isomerase, cytosolic/cyclophilin AT2G17130 isocitrate dehydrogenase subunit 2/NAD+ isocitrate dehydrogenase subunit 2 AT2G18700 glycosyl transferase family 20 protein AT2G19070 transferase family protein AT2G19210 leucine-rich repeat protein kinase, putative AT2G20330 transducin family protein/WD-40 repeat family protein AT2G20420 succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial, putative AT2G20580 26S proteasome regulatory subunit S2 (RPN1) AT2G20805 hypothetical protein AT2G21170 triosephosphate isomerase, chloroplast, putative AT2G21390 coatomer protein complex, subunit alpha, putative AT2G21410 vacuolar proton ATPase, putative AT2G21920 hypothetical protein (Fragment) AT2G22230 beta-hydroxyacyl-ACP dehydratase, putative AT2G23930 small nuclear ribonucleoprotein G, putative AT2G24420 DNA repair ATPase-related contains 2 transmembrane domains AT2G26570 expressed protein AT2G26890 DNAJ heat shock N-terminal domain-containing protein AT2G27030 calmodulin AT2G27610 pentatricopeptide (PPR) repeat-containing protein AT2G27870 hypothetical protein AT2G28000 RuBisCO subunit binding-protein alpha subunit, chloroplast AT2G28620 kinesin motor protein-related AT2G29540 DNA-directed RNA polymerase I(A) and III(C) 14 kDa subunit (RPAC14) AT2G31680 Ras-related GTP-binding protein, putative AT2G32240 putative myosin heavy chain AT2G33210 chaperonin, putative AT2G33730 DEAD box RNA helicase, putative AT2G34170 expressed protein AT2G35605 SWIB complex BAF60b domain-containing protein AT2G36060 ubiquitin-conjugating enzyme family protein AT2G36260 iron-sulfur cluster assembly complex protein, putative AT2G36460 fructose-bisphosphate aldolase, putative AT2G36810 expressed protein AT2G37230 pentatricopeptide (PPR) repeat-containing protein AT2G37420 kinesin motor protein-related AT2G38560 transcription factor S-II (TFIIS) domain-containing protein AT2G38810 histone H2A, putative AT2G39730 ribulose bisphosphate carboxylase/oxygenase activase AT2G39990 eukaryotic translation initiation factor 3 subunit 5 AT2G40070 expressed protein AT2G40270 protein kinase family protein AT2G41450 GCN5-related N-acetyltransferase (GNAT) family protein AT2G41800 expressed protein AT2G42230 tubulin-specific chaperone C-related AT2G42450 lipase class 3 family protein AT2G42520 DEAD box RNA helicase, putative AT2G43160 epsin N-terminal homology (ENTH) domain-containing protein AT2G43750 cysteine synthase, chloroplast/O-acetylserine (thiol)-lyase AT2G44060 late embryogenesis abundant family protein/LEA family protein AT2G45030 mitochondrial elongation factor, putative AT2G45620 nucleotidyltransferase family protein AT2G46520 cellular apoptosis susceptibility protein, putative/importin- alpha AT2G47110 ubiquitin extension protein 6 (UBQ6)/40S ribosomal protein S27A AT3G01040 glycosyl transferase family 8 protein AT3G01720 expressed protein AT3G01740 expressed protein AT3G02200 proteasome family protein AT3G02230 reversibly glycosylated polypeptide-1 AT3G02500 unknown protein AT3G02530 chaperonin, putative AT3G02650 pentatricopeptide (PPR) repeat-containing protein AT3G03300 DEAD/DEAH box helicase carpel factory-related AT3G03780 AtMS2|AtMS2 (Arabidopsis thaliana methionine synthase 2) AT3G03960 chaperonin, putative AT3G04120 glyceraldehyde-3-phosphate dehydrogenase, cytosolic AT3G05810 expressed protein AT3G07160 glycosyl transferase family 48 protein AT3G07630 prephenate dehydratase family protein AT3G07810 heterogeneous nuclear ribonucleoprotein, putative AT3G08030 expressed protein AT3G08530 clathrin heavy chain, putative AT3G08590 2,3-biphosphoglycerate-independent phosphoglycerate mutase, putative AT3G09170 Ulp1 protease family protein AT3G09350 armadillo/beta-catenin repeat family protein AT3G09440 heat shock cognate 70 kDa protein 3 AT3G10310 kinesin motor protein-related AT3G10860 ubiquinol-cytochrome C reductase complex ubiquinone- binding protein AT3G11130 clathrin heavy chain, putative AT3G11400 eukaryotic translation initiation factor 3G AT3G11770 expressed protein AT3G11950 ATHST; prenyltransferase AT3G12580 heat shock protein 70, putative AT3G12800 short-chain dehydrogenase/reductase (SDR) family protein AT3G13160 pentatricopeptide (PPR) repeat-containing protein AT3G13460 expressed protein AT3G13470 chaperonin, putative AT3G13920 eukaryotic translation initiation factor 4A-1 AT3G14990 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis protein AT3G15020 malate dehydrogenase [NAD], mitochondrial, putative AT3G16230 expressed protein similar to ASC-1 complex subunit P50 AT3G16270 expressed protein AT3G16540 DegP protease, putative AT3G16640 translationally controlled tumor family protein AT3G17300 expressed protein AT3G17360 kinesin motor protein-related similar to KLP2 protein AT3G17390 S-adenosylmethionine synthetase, putative AT3G18000 phosphoethanolamine N-methyltransferase 1 AT3G18190 chaperonin, putative AT3G18530 expressed protein AT3G19050 kinesin motor protein-related AT3G20670 histone H2A, putative AT3G20780 topoisomerase 6 subunit B (TOP6B) AT3G21070 ATP-NAD kinase family protein AT3G22330 DEAD box RNA helicase, putative AT3G22890 sulfate adenylyltransferase 1/ATP-sulfurylase 1 AT3G23990 chaperonin (CPN60) (HSP60) AT3G24890 synaptobrevin-related AT3G26020 serine/threonine protein phosphatase 2A (PP2A) regulatory subunit B′, putative AT3G26380 glycosyl hydrolase family protein 27 AT3G27400 pectate lyase family protein AT3G28925 hypothetical protein AT3G42100 AT hook motif-containing protein-related AT3G42270 putative protein AT3G43300 guanine nucleotide exchange family protein AT3G43810 calmodulin AT3G45770 oxidoreductase, zinc-binding dehydrogenase family protein AT3G46560 mitochondrial import inner membrane translocase (TIM9) AT3G46990 hypothetical protein AT3G47850 expressed protein AT3G48250 pentatricopeptide (PPR) repeat-containing protein AT3G48670 XH/XS domain-containing protein/XS zinc finger domain- containing protein AT3G48870 ATP-dependent Clp protease ATP-binding subunit (ClpC) AT3G49640 nitrogen regulation family protein AT3G50280 transferase family protein AT3G50370 expressed protein AT3G51150 kinesin motor family protein AT3G51570 disease resistance protein (TIR-NBS-LRR class), putative AT3G51950 zinc finger (CCCH-type) family protein/RNA recognition motif (RRM) AT3G52140 tetratricopeptide repeat (TPR)-containing protein AT3G52930 fructose-bisphosphate aldolase, putative AT3G54360 expressed protein DNA-binding Mel-18 protein AT3G54610 histone acetyltransferase (GCN5) AT3G54940 cysteine proteinase, putative AT3G55000 Tonneau 1a AT3G55005 Tonneau 1b AT3G55290 short-chain dehydrogenase/reductase (SDR) family protein AT3G55310 short-chain dehydrogenase/reductase (SDR) family protein AT3G55460 SC35-like splicing factor, 30 kD (SCL30) AT3G55770 LIM domain-containing protein AT3G57290 eukaryotic translation initiation factor 3E AT3G58510 DEAD box RNA helicase, putative (RH11) AT3G58610 ketol-acid reductoisomerase AT3G59760 cysteine synthase, mitochondrial, putative AT3G62010 expressed protein AT3G62250 ubiquitin extension protein 5 (UBQ5)/40S ribosomal protein S27A AT4G00020 BRCA2 repeat-containing protein AT4G01290 expressed protein AT4G01800 preprotein translocase secA subunit, putative AT4G02930 elongation factor Tu, putative AT4G03550 glycosyl transferase family 48 protein AT4G11150 vacuolar ATP synthase subunit E AT4G11420 eukaryotic translation initiation factor 3 subunit 10 AT4G12130 glycine cleavage T family protein AT4G12770 auxilin-related AT4G12780 auxilin-like protein AT4G14060 major latex protein-related AT4G14130 xyloglucan:xyloglucosyl transferase, putative AT4G14140 DNA (cytosine-5-)-methyltransferase (METII) AT4G14260 hypothetical protein AT4G15640 expressed protein AT4G15760 monooxygenase, putative (MO1) AT4G17150 unknown protein AT4G17440 expressed protein AT4G17720 RNA recognition motif (RRM)-containing protein AT4G18040 eukaryotic translation initiation factor 4E 1 AT4G18080 hypothetical protein AT4G19530 disease resistance protein (TIR-NBS-LRR class), putative AT4G20160 expressed protein AT4G20360 elongation factor Tu AT4G20980 eukaryotic translation initiation factor 3 subunit 7, putative AT4G23670 major latex protein-related AT4G23850 long-chain-fatty-acid--CoA ligase/long-chain acyl-CoA synthetase AT4G24100 protein kinase family protein AT4G24280 heat shock protein 70, putative AT4G24760 expressed protein AT4G25580 stress-responsive protein-related AT4G26900 imidazole glycerol phosphate synthase hisHF, chloroplast AT4G27440 protochlorophyllide reductase B, chloroplast AT4G28400 protein phosphatase 2C, putative AT4G29800 patatin-related low similarity to patatin precursor AT4G31805 WRKY family transcription factor AT4G31820 phototropic-responsive NPH3 family protein AT4G31990 aspartate aminotransferase, chloroplast/transaminase A (ASP5) (AAT1) AT4G32500 potassium channel protein, putative AT4G32551 WD-40 repeat family protein (LEUNIG) AT4G33200 myosin, putative AT4G34290 SWIB complex BAF60b domain-containing protein AT4G34350 LytB family protein AT4G35260 isocitrate dehydrogenase subunit 1/NAD+ isocitrate dehydrogenase subunit 1 AT4G35650 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative AT4G35890 La domain-containing protein AT4G35970 L-ascorbate peroxidase, putative AT4G36960 RNA recognition motif (RRM)-containing protein AT4G37420 hypothetical protein AT4G37580 N-acetyltransferase, putative/hookless1 (HLS1) AT4G37910 heat shock protein 70, mitochondrial, putative AT4G38030 hypothetical protein AT4G38070 bHLH family protein AT4G39580 kelch repeat-containing F-box family protein AT5G01010 expressed protein AT5G02490 heat shock cognate 70 kDa protein 2 AT5G02500 heat shock cognate 70 kDa protein 1 AT5G02590 chloroplast lumen common family protein AT5G03340 cell division cycle protein 48, putative AT5G03650 1,4-alpha-glucan branching enzyme AT5G03690 fructose-bisphosphate aldolase, putative AT5G04590 sulfite reductase/ferredoxin AT5G05370 ubiquinol-cytochrome C reductase complex ubiquinone- binding protein AT5G05640 nucleoprotein-related AT5G05780 26S proteasome non-ATPase regulatory subunit 7, putative AT5G06140 phox (PX) domain-containing protein AT5G06400 pentatricopeptide (PPR) repeat-containing protein AT5G06450 expressed protein AT5G06850 anthranilate phosphoribosyltransferase-like protein AT5G08415 lipoic acid synthase family protein AT5G08670 ATP synthase beta chain, mitochondrial AT5G08680 ATP synthase beta chain, mitochondrial AT5G08690 ATP synthase beta chain, mitochondrial AT5G09590 heat shock protein 70 AT5G09900 26S proteasome regulatory subunit, putative (RPN5) AT5G10160 beta-hydroxyacyl-ACP dehydratase, putative AT5G11110 sucrose-phosphate synthase-like protein AT5G11340 GCN5-related N-acetyltransferase (GNAT) family protein AT5G12010 expressed protein AT5G12240 expressed protein AT5G12310 zinc finger (C3HC4-type RING finger) family protein AT5G13130 hypothetical protein low similarity to microrchidia AT5G14040 mitochondrial phosphate transporter AT5G15580 expressed protein AT5G15610 proteasome family protein AT5G15650 reversibly glycosylated polypeptide-2 AT5G15920 structural maintenance of chromosomes (SMC) family protein AT5G16070 chaperonin, putative AT5G17680 disease resistance protein (TIR-NBS-LRR class), putative AT5G17890 LIM domain-containing protein/disease resistance protein- related AT5G17920 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase AT5G18110 novel cap-binding protein (nCBP) AT5G18730 hypothetical protein AT5G19310 homeotic gene regulator, putative AT5G19550 aspartate aminotransferase, cytoplasmic isozyme 1/transaminase A AT5G20010 Ras-related GTP-binding nuclear protein AT5G20020 Ras-related GTP-binding nuclear protein AT5G20360 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein (Fragment) AT5G20720 20 kDa chaperonin, chloroplast AT5G20890 chaperonin, putative AT5G21274 calmodulin AT5G22650 expressed protein AT5G23540 26S proteasome regulatory subunit, putative AT5G23890 expressed protein AT5G23930 mitochondrial transcription termination factor-related AT5G24710 WD-40 repeat family protein AT5G25230 elongation factor Tu family protein AT5G25940 early nodulin-related AT5G26200 mitochondrial substrate carrier family protein AT5G26710 glutamate-tRNA ligase, putative AT5G26742 DEAD box RNA helicase (RH3) AT5G26800 expressed protein AT5G27390 expressed protein AT5G27920 F-box family protein AT5G28430 hypothetical protein AT5G28540 luminal binding protein 1 AT5G28850 calcium-binding EF hand family protein AT5G35360 acetyl-CoA carboxylase, biotin carboxylase subunit (CAC2) AT5G35620 eukaryotic translation initiation factor 4E 2 AT5G36670 putative protein AT5G37150 tRNA-splicing endonuclease positive effector-related AT5G37470 hypothetical protein AT5G37510 NADH-ubiquinone dehydrogenase, mitochondrial, putative AT5G39320 UDP-glucose 6-dehydrogenase, putative AT5G40060 disease resistance protein (TIR-NBS-LRR class), putative AT5G40760 glucose-6-phosphate 1-dehydrogenase/G6PD AT5G42020 luminal binding protein 2 AT5G42080 GTP-binding protein/phragmoplastin, putative AT5G42950 GYF domain-containing protein AT5G42980 thioredoxin H-type 3 AT5G43780 sulfate adenylyltransferase 4/ATP-sulfurylase 4 AT5G44320 eukaryotic translation initiation factor 3 subunit 7, putative AT5G44510 disease resistance protein (TIR-NBS-LRR class), putative (TAO1) AT5G45060 disease resistance protein (TIR-NBS-LRR class), putative AT5G45140 DNA-directed RNA polymerase, putative AT5G47460 pentatricopeptide (PPR) repeat-containing protein AT5G47890 NADH-ubiquinone oxidoreductase B8 subunit, putative AT5G48620 disease resistance protein (CC-NBS-LRR class), putative (Fragment) AT5G49030 tRNA synthetase class I (I, L, M and V) family protein AT5G49910 heat shock protein 70 AT5G50370 adenylate kinase, putative AT5G50810 mitochondrial import inner membrane translocase (TIM8) AT5G50920 ATP-dependent Clp protease ATP-binding subunit (ClpC) AT5G51000 F-box family protein AT5G51670 expressed protein AT5G51795 Kin17 DNA-binding protein-related (Fragment) AT5G52040 arginine/serine-rich splicing factor RSP41 (RSP41) AT5G52400 cytochrome P450 family protein AT5G53460 glutamate synthase [NADH], chloroplast, putative AT5G54640 histone H2A AT5G54670 kinesin-like protein C (KATC) AT5G55190 Ras-related GTP-binding nuclear protein AT5G56000 heat shock protein 81 AT5G56030 heat shock protein 81 AT5G56500 chaperonin, putative AT5G57350 ATPase 3, plasma membrane-type/proton pump 3 AT5G58070 lipocalin, putative similar to temperature stress-induced lipocalin AT5G59220 protein phosphatase 2C, putative AT5G59620 putative protein AT5G59880 actin-depolymerizing factor 3 (ADF3) AT5G60390 elongation factor 1-alpha AT5G60720 expressed protein AT5G60980 nuclear transport factor 2 (NTF2) family protein AT5G61780 tudor domain-containing protein/nuclease family protein AT5G63020 disease resistance protein (CC-NBS-LRR class), putative AT5G63400 adenylate kinase AT5G63800 glycosyl hydrolase family 35 protein AT5G64760 26S proteasome regulatory subunit, putative (RPN5) AT5G66470 expressed protein

TABLE 3 Overrepresentation of Biological Processes among the preys of the core (A) and non-core (B) dataset as determined with the Cytoscape plugin BiNGO. A. Overrepresentation of Biological Processes among the preys of the core dataset. Search parameters: File created with BiNGO (c) on 22-okt-2008 at 16:17:17 ontology: process curator: GO Selected ontology file: BiNGO.jar!/GO_Biological_Process Selected annotation file: gene_association_2008okt04.tair Overrepresentation Selected statistical test: Hypergeometric test Selected correction: Benjamini & Hochberg False Discovery Rate (FDR) correction Selected significance level: 0.05 Testing option: Test cluster versus whole annotation Number of annotated genes in selection: 137 Number of annotated genes in network/whole annotation: 25557 Results: corr # GO-ID p-value p-value selected # total Description 7049 2.30E−34 7.17E−32 28 164 cell cycle 51726 1.11E−28 1.74E−26 21 93 regulation of cell cycle 6260 2.09E−18 2.17E−16 16 116 DNA replication 6263 4.33E−18 3.38E−16 13 58 DNA-dependent DNA replication 74 8.10E−15 5.05E−13 9 26 regulation of progression through cell cycle 6259 7.00E−14 3.60E−12 21 463 DNA metabolism 43285 8.43E−14 3.60E−12 18 312 biopolymer catabolism 30163 9.23E−14 3.60E−12 17 268 protein catabolism 9057 3.38E−13 1.10E−11 19 390 macromolecule catabolism 6511 4.22E−13 1.10E−11 16 249 ubiquitin-dependent protein catabolism 43632 4.22E−13 1.10E−11 16 249 modification-dependent macromolecule catabolism 19941 4.22E−13 1.10E−11 16 249 modification-dependent protein catabolism 51603 4.77E−13 1.15E−11 16 251 proteolysis during cellular protein catabolism 44257 6.86E−13 1.53E−11 16 257 cellular protein catabolism 44265 1.05E−12 2.19E−11 18 362 cellular macromolecule catabolism 79 4.38E−12 8.55E−11 6 10 regulation of cyclin-dependent protein kinase activity 6270 1.91E−11 3.51E−10 6 12 DNA replication initiation 278 3.69E−11 6.40E−10 8 40 mitotic cell cycle 6469 2.27E−10 3.38E−09 5 8 negative regulation of protein kinase activity 45736 2.27E−10 3.38E−09 5 8 negative regulation of cyclin-dependent protein kinase activity 51348 2.27E−10 3.38E−09 5 8 negative regulation of transferase activity 8151 2.45E−10 3.47E−09 97 11293 cellular physiological process 9056 3.36E−10 4.55E−09 19 582 catabolism 45786 5.09E−10 6.62E−09 5 9 negative regulation of progression through cell cycle 42023 5.44E−10 6.79E−09 6 19 DNA endoreduplication 43086 1.01E−09 1.22E−08 5 10 negative regulation of enzyme activity 44248 1.30E−09 1.50E−08 18 560 cellular catabolism 43283 1.38E−09 1.54E−08 48 3695 biopolymer metabolism 45859 1.99E−09 2.04E−08 6 23 regulation of protein kinase activity 43549 1.99E−09 2.04E−08 6 23 regulation of kinase activity 9987 2.03E−09 2.04E−08 98 11858 cellular process 51338 2.64E−09 2.58E−08 6 24 regulation of transferase activity 50794 6.88E−09 6.51E−08 33 2040 regulation of cellular process 51325 7.92E−09 7.06E−08 5 14 interphase 51329 7.92E−09 7.06E−08 5 14 interphase of mitotic cell cycle 51244 1.26E−08 1.09E−07 32 1980 regulation of cellular physiological process 50791 3.60E−08 3.04E−07 32 2070 regulation of physiological process 7582 1.33E−07 1.09E−06 100 13066 physiological process 50789 2.21E−07 1.77E−06 33 2359 regulation of biological process 50790 2.72E−07 2.12E−06 7 81 regulation of catalytic activity 6139 6.29E−07 4.79E−06 37 2974 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 43170 1.23E−06 9.17E−06 60 6396 macromolecule metabolism 6508 1.61E−06 1.17E−05 16 718 proteolysis 51302 1.24E−05 8.77E−05 3 9 regulation of cell division 44238 1.87E−05 1.30E−04 69 8433 primary metabolism 51510 2.85E−05 1.93E−04 2 2 regulation of unidimensional cell growth 44237 1.45E−04 9.61E−04 67 8584 cellular metabolism 80 1.70E−04 1.06E−03 2 4 G1 phase of mitotic cell cycle 82 1.70E−04 1.06E−03 2 4 G1/S transition of mitotic cell cycle 51318 1.70E−04 1.06E−03 2 4 G1 phase 7346 2.82E−04 1.73E−03 2 5 regulation of progression through mitotic cell cycle 48856 3.80E−04 2.28E−03 17 1248 anatomical structure development 48519 4.57E−04 2.69E−03 6 182 negative regulation of biological process 9653 5.58E−04 3.22E−03 10 526 morphogenesis 51243 6.65E−04 3.72E−03 5 129 negative regulation of cellular physiological process 51301 6.67E−04 3.72E−03 3 32 cell division 48523 6.89E−04 3.77E−03 5 130 negative regulation of cellular process 1558 7.82E−04 4.21E−03 2 8 regulation of cell growth 43118 1.02E−03 5.42E−03 5 142 negative regulation of physiological process 6281 1.09E−03 5.67E−03 5 144 DNA repair 9793 1.28E−03 6.56E−03 9 487 embryonic development (sensu Magnoliophyta) 6974 1.47E−03 7.39E−03 5 154 response to DNA damage stimulus 9790 2.01E−03 9.94E−03 9 520 embryonic development 48316 2.28E−03 1.11E−02 9 530 seed development 48272 2.32E−03 1.11E−02 3 49 trichome morphogenesis (sensu Magnoliophyta) 48608 2.37E−03 1.12E−02 9 533 reproductive structure development 7148 2.43E−03 1.13E−02 6 252 cell morphogenesis 6457 2.58E−03 1.18E−02 6 255 protein folding 904 2.60E−03 1.18E−02 3 51 cellular morphogenesis during differentiation 7017 2.66E−03 1.19E−02 4 107 microtubule-based process 7275 2.81E−03 1.23E−02 19 1765 development 9965 2.94E−03 1.27E−02 4 110 leaf morphogenesis 7018 3.23E−03 1.37E−02 3 55 microtubule-based movement 9934 3.26E−03 1.37E−02 2 16 regulation of meristem organization 8152 3.29E−03 1.37E−02 70 10044 metabolism 19952 3.72E−03 1.53E−02 11 794 reproduction 48827 3.90E−03 1.58E−02 5 193 phyllome development 16043 3.95E−03 1.58E−02 16 1420 cell organization and biogenesis 9117 4.64E−03 1.83E−02 4 125 nucleotide metabolism 35315 4.95E−03 1.91E−02 3 64 hair cell differentiation 10026 4.95E−03 1.91E−02 3 64 trichome differentiation (sensu Magnoliophyta) 51446 5.36E−03 2.02E−02 1 1 positive regulation of progression through meiotic cell cycle 51445 5.36E−03 2.02E−02 1 1 regulation of progression through meiotic cell cycle 30154 5.56E−03 2.07E−02 5 210 cell differentiation 9887 5.67E−03 2.08E−02 5 211 organ morphogenesis 30705 6.86E−03 2.49E−02 3 72 cytoskeleton-dependent intracellular transport 48468 8.86E−03 3.18E−02 3 79 cell development 10016 8.97E−03 3.18E−02 4 151 shoot morphogenesis 7276 9.80E−03 3.44E−02 4 155 gametogenesis 7050 1.07E−02 3.51E−02 1 2 cell cycle arrest 42276 1.07E−02 3.51E−02 1 2 error-prone postreplication DNA repair 86 1.07E−02 3.51E−02 1 2 G2/M transition of mitotic cell cycle 45020 1.07E−02 3.51E−02 1 2 error-prone DNA repair 184 1.07E−02 3.51E−02 1 2 mRNA catabolism, nonsense-mediated decay 6358 1.07E−02 3.51E−02 1 2 regulation of global transcription from RNA polymerase II promoter 46907 1.10E−02 3.58E−02 7 451 intracellular transport 9165 1.15E−02 3.70E−02 3 87 nucleotide biosynthesis 51649 1.18E−02 3.75E−02 7 457 establishment of cellular localization 51641 1.27E−02 3.93E−02 7 464 cellular localization 9744 1.27E−02 3.93E−02 2 32 response to sucrose stimulus 40008 1.27E−02 3.93E−02 2 32 regulation of growth 48366 1.59E−02 4.76E−02 4 179 leaf development 16288 1.60E−02 4.76E−02 2 36 cytokinesis 10071 1.60E−02 4.76E−02 1 3 root meristem specification 48367 1.60E−02 4.76E−02 5 273 shoot development B. Overrepresentation of Biological Processes among the preys of the non-core dataset. Search parameters: File created with BiNGO (c) on 22-okt-2008 at 16:28:37 ontology: process curator: GO Selected ontology file: BiNGO.jar!/GO_Biological_Process Selected annotation file: gene_association_2008okt04.tair Overrepresentation Selected statistical test: Hypergeometric test Selected correction: Benjamini & Hochberg False Discovery Rate (FDR) correction Selected significance level: 0.05 Testing option: Test cluster versus whole annotation Number of annotated genes in selection: 197 Number of annotated genes in network/whole annotation: 25538 Results: corr # GO-ID p-value p-value selected # total Description 46686 5.78E−13 3.14E−10 22 396 response to cadmium ion 10038 4.07E−12 1.11E−09 22 437 response to metal ion 10035 9.76E−12 1.77E−09 22 457 response to inorganic substance 7049 4.69E−11 6.38E−09 14 166 cell cycle 51726 2.75E−09 2.99E−07 10 93 regulation of cell cycle 42221 1.01E−08 9.16E−07 38 1789 response to chemical stimulus 6259 2.22E−08 1.73E−06 18 462 DNA metabolism 8151 8.57E−08 5.83E−06 124 11291 cellular physiological process 50896 1.42E−07 8.56E−06 56 3617 response to stimulus 9987 2.38E−07 1.29E−05 127 11856 cellular process 42023 2.76E−07 1.36E−05 5 19 DNA endoreduplication 6263 3.15E−07 1.36E−05 7 58 DNA-dependent DNA replication 6260 3.24E−07 1.36E−05 9 117 DNA replication 6950 8.79E−07 3.42E−05 28 1300 response to stress 74 1.50E−06 5.43E−05 5 26 regulation of progression through cell cycle 7582 2.21E−06 7.53E−05 133 13063 physiological process 6970 2.77E−06 8.87E−05 14 397 response to osmotic stress 6139 6.40E−06 1.94E−04 45 2973 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 9056 1.27E−05 3.64E−04 16 582 catabolism 9628 2.56E−05 6.96E−04 23 1140 response to abiotic stimulus 9651 3.21E−05 7.96E−04 12 369 response to salt stress 44248 3.22E−05 7.96E−04 15 560 cellular catabolism 6454 3.40E−05 8.04E−04 6 79 translational initiation 79 5.21E−05 1.18E−03 3 10 regulation of cyclin-dependent protein kinase activity 9057 5.47E−05 1.19E−03 12 390 macromolecule catabolism 51510 5.92E−05 1.24E−03 2 2 regulation of unidimensional cell growth 44237 8.90E−05 1.79E−03 92 8580 cellular metabolism 15980 1.10E−04 2.15E−03 7 140 energy derivation by oxidation of organic compounds 44265 1.25E−04 2.35E−03 11 362 cellular macromolecule catabolism 45333 1.33E−04 2.41E−03 4 34 cellular respiration 43283 1.51E−04 2.66E−03 48 3692 biopolymer metabolism 9826 1.63E−04 2.77E−03 7 149 unidimensional cell growth 43044 1.77E−04 2.91E−03 2 3 ATP-dependent chromatin remodeling 7275 2.23E−04 3.56E−03 28 1765 development 278 2.53E−04 3.93E−03 4 40 mitotic cell cycle 9266 3.13E−04 4.74E−03 10 338 response to temperature stimulus 9719 4.96E−04 7.30E−03 20 1131 response to endogenous stimulus 6084 5.43E−04 7.77E−03 3 21 acetyl-CoA metabolism 6561 5.83E−04 8.05E−03 2 5 proline biosynthesis 9737 5.92E−04 8.05E−03 8 241 response to abscisic acid stimulus 40007 6.59E−04 8.74E−03 8 245 growth 45859 7.14E−04 9.04E−03 3 23 regulation of protein kinase activity 43549 7.14E−04 9.04E−03 3 23 regulation of kinase activity 43285 7.46E−04 9.23E−03 9 312 biopolymer catabolism 7148 7.91E−04 9.46E−03 8 252 cell morphogenesis 51338 8.12E−04 9.46E−03 3 24 regulation of transferase activity 6092 8.18E−04 9.46E−03 5 94 main pathways of carbohydrate metabolism 16049 9.82E−04 1.11E−02 7 201 cell growth 43170 1.08E−03 1.20E−02 69 6392 macromolecule metabolism 8361 1.13E−03 1.23E−02 7 206 regulation of cell size 30163 1.17E−03 1.24E−02 8 268 protein catabolism 50789 1.18E−03 1.24E−02 32 2359 regulation of biological process 50791 1.26E−03 1.30E−02 29 2070 regulation of physiological process 6091 1.29E−03 1.30E−02 8 272 generation of precursor metabolites and energy 51244 1.34E−03 1.33E−02 28 1980 regulation of cellular physiological process 16043 1.47E−03 1.42E−02 22 1419 cell organization and biogenesis 6560 1.61E−03 1.42E−02 2 8 proline metabolism 6469 1.61E−03 1.42E−02 2 8 negative regulation of protein kinase activity 45736 1.61E−03 1.42E−02 2 8 negative regulation of cyclin-dependent protein kinase activity 51348 1.61E−03 1.42E−02 2 8 negative regulation of transferase activity 1558 1.61E−03 1.42E−02 2 8 regulation of cell growth 48856 1.64E−03 1.42E−02 20 1248 anatomical structure development 9725 1.65E−03 1.42E−02 14 729 response to hormone stimulus 44238 1.81E−03 1.53E−02 85 8429 primary metabolism 8152 1.82E−03 1.53E−02 98 10040 metabolism 9409 1.92E−03 1.59E−02 7 226 response to cold 45786 2.06E−03 1.64E−02 2 9 negative regulation of progression through cell cycle 51302 2.06E−03 1.64E−02 2 9 regulation of cell division 50794 2.08E−03 1.64E−02 28 2040 regulation of cellular process 51170 2.27E−03 1.76E−02 3 34 nuclear import 9790 2.47E−03 1.89E−02 11 520 embryonic development 43086 2.56E−03 1.93E−02 2 10 negative regulation of enzyme activity 6395 2.59E−03 1.93E−02 4 74 RNA splicing 6099 3.11E−03 2.26E−02 2 11 tricarboxylic acid cycle 46356 3.11E−03 2.26E−02 2 11 acetyl-CoA catabolism 6511 3.30E−03 2.30E−02 7 249 ubiquitin-dependent protein catabolism 43632 3.30E−03 2.30E−02 7 249 modification-dependent macromolecule catabolism 19941 3.30E−03 2.30E−02 7 249 modification-dependent protein catabolism 51603 3.45E−03 2.37E−02 7 251 proteolysis during cellular protein catabolism 6270 3.71E−03 2.53E−02 2 12 DNA replication initiation 9064 3.88E−03 2.55E−02 3 41 glutamine family amino acid metabolism 9615 3.88E−03 2.55E−02 3 41 response to virus 44257 3.92E−03 2.55E−02 7 257 cellular protein catabolism 48827 3.94E−03 2.55E−02 6 193 phyllome development 51169 4.16E−03 2.66E−02 3 42 nuclear transport 16071 4.40E−03 2.78E−02 5 138 mRNA metabolism 9793 4.72E−03 2.95E−02 10 487 embryonic development (sensu Magnoliophyta) 9109 5.07E−03 3.13E−02 2 14 coenzyme catabolism 6800 5.22E−03 3.19E−02 7 271 oxygen and reactive oxygen species metabolism 398 5.38E−03 3.25E−02 3 46 nuclear mRNA splicing, via spliceosome 48367 5.43E−03 3.25E−02 7 273 shoot development 6096 5.71E−03 3.38E−02 3 47 glycolysis 9060 5.82E−03 3.40E−02 2 15 aerobic respiration 375 6.06E−03 3.47E−02 3 48 RNA splicing, via transesterification reactions 377 6.06E−03 3.47E−02 3 48 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 9084 7.46E−03 4.23E−02 2 17 glutamine family amino acid biosynthesis 42891 7.71E−03 4.24E−02 1 1 antibiotic transport 7091 7.71E−03 4.24E−02 1 1 mitotic metaphase/anaphase transition 30071 7.71E−03 4.24E−02 1 1 regulation of mitotic metaphase/anaphase transition 48316 8.36E−03 4.55E−02 10 530 seed development 48608 8.68E−03 4.68E−02 10 533 reproductive structure development 19952 8.92E−03 4.76E−02 13 794 reproduction 6732 9.45E−03 4.99E−02 5 166 coenzyme metabolism

TABLE 4 Overview of cell cycle-related features used in the computational analysis to search for new cell cycle proteins. Cell cycle feature Category # of genes References Periodicity Gene expression 1258 (5, 6) MSA-like Promotor motif 2295 (7) E2Fa-like Promotor motif 1809 (7) E2F10SPCNA Promotor motif 2221 (7) OS_motifslandIIa Promotor motif 2310 (7) UP1ATMSD Promotor motif 3738 (7) wrrmGCGn Promotor motif 2179 (7) CDK consensus site Phosphorylation motif 6321 (8) [IM]R-tail Protein sequence motif 116 (16, 17) PEST-sequence Destruction motif 2719 (18)  D-box Destruction motif 2369 (19)  KEN-box Destruction motif 410 (19)  GxEN-box Destruction motif 300 (20)  A-box Destruction motif 1779 (21) 

TABLE 5 collection of cell cycle genes. Collection of 518 genes annotated as cell cycle by gene ontology, including all genes described as core cell cycle genes or related to cell cycle (19, 22-24). The following GO terms were used to build the collection: cell cycle (GO: 0007049), cell division (GO: 0051301), cell proliferation (GO: 0008283), chromosome segregation (GO: 0007059), DNA replication (GO: 0006260), DNA replication and chromosome cycle (GO: 0000067). For every gene, the number of cell cycle-related features present is shown. This collection was subtracted from the prey lists to find novel cell cycle proteins. Accession number Name # features AT2G31270 CDT1a 8 AT5G13840 CCS52B 7 AT3G16320 cdc27a 7 AT1G07270 cdc6b 7 AT3G59550 cohesion family protein SYN3 (SYN3) 7 AT5G25380 CYCA2; 1 7 AT3G11450 DNAJ HEAT SHOCK N-TERMINAL DOMAIN-CONTAINING PROTEIN/ 7 CELL DIVISION PROTEIN-RELATED AT1G65470 chromatin assembly factor-1 (FASCIATA1) (FAS1), identical to FAS1 6 (Arabidopsis thaliana) GI: 4887626 AT1G77390 CYCA1; 2 6 AT5G43080 CYCA3; 1 6 AT3G11520 CYCB1; 3 6 AT3G10690 DNA gyrase subunit A family protein 6 AT4G25540 DNA mismatch repair protein MSH3; AtMsh3 6 AT1G47870 E2Fc 6 AT4G38600 KAK (KAKTUS) 6 AT5G46280 MCM3 6 AT5G07280 receptor-like protein kinase-like protein; receptor-like protein kinase - 6 lpomoea nil (Japanese morning glory), PIR: T18536 AT5G61000 Replication protein A1; Putative RNA helicase 6 AT5G42190 ASK2 (ARABIDOPSIS SKP1-LIKE 2); UBIQUITIN-PROTEIN LIGASE 5 AT2G29680 cdc6 5 AT1G18670 CKL3 5 AT1G70210 CYCD1; 1 5 AT4G37630 CYCD5; 1 5 AT5G49160 DNA (cytosine-5-)-methyltransferase (AtHIM), identical to SP: P34881 5 DNA (cytosine-5)-methyltransferase AthI (EC 2.1.1.37) {Arabidopsis thaliana} AT1G08130 DNA ligase/polydeoxyribonucleotide synthase [AtP] identical to 5 SP|Q42572 DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [AtP]) {Arabidopsis thaliana}; contains Pfam profiles: PF01068 AtP dependent DNA ligase domain, PF04679 AtP dependent DNA AT5G41880 DNA polymerase alpha subunit IV (Primase)-like protein 5 AT3G13170 DNA TOPOISOMERASE VIA (SPO11-1), IDENTICAL TO ATSPO11-1 5 (ARABIDOPSIS THALIANA) GI: 13383478; CONTAINS PFAM PROFILE PF04406: TYPE IIB DNA TOPOISOMERASE; IDENTICAL TO CDNA PUTATIVE TOPOISOMERASE VIA (SPO11 GENE 1) GI: 7270974|CHR3: 4231567-4234199 REVERSE|ALIASES: MJG19.19 AT5G67100 DNA-directed DNA polymerase alpha catalytic subunit, putative, similar 5 to SP: O48653 DNA polymerase alpha catalytic subunit (EC 2.7.7.7) {Oryza sativa}; contains Pfam profiles: PF03175 DNA polymerase type B, organellar and viral, PF00136 DNA polymerase fa AT5G02470 DPa 5 AT5G22220 E2Fb 5 AT3G43210 kinesin motor family protein (NACK2) 5 AT1G18800 NRP2 (NAP1-RELATED PROTEIN 2); DNA BINDING/CHROMATIN 5 BINDING/HISTONE BINDING AT2G37560 ORC2 5 AT1G26840 ORC6 5 AT5G16270 Rad21/Rec8-like family protein weak similarity to cohesion family 5 protein SYN2 [Arabidopsis thaliana] gI: 12006360; contains Pfam profiles PF04824: Conserved region of Rad21/Rec8 like protein, PF04825: N terminus of Rad21/Rec8 like protein; supporting AT3G12280 RBR 5 AT5G61210 SNAP33 (SYNAPTOSOMAL-ASSOCIATED PROTEIN 33); T-SNARE 5 AT5G48600 structural maintenance of chromosomes (SMC) family protein, similar 5 to SP: P50532 Chromosome assembly protein XCAP-C {Xenopus laevis}; contains Pfam profiles PF02483: SMC family C-terminal domain, PF02463: RecF/RecN/SMC N terminal domain AT5G55220 trigger factor type chaperone family protein, contains Pfam profiles 5 PF05697: Bacterial trigger factor protein (TF), PF05698: Bacterial trigger factor protein (TF) C-terminus, PF00254: peptidyl-prolyl cis-trans isomerase, FKBP-type AT3G60740 tubulin folding cofactor D 5 AT3G19770 vacuolar sorting protein 9 domain-containing protein 5 AT5G05560 APC1 4 AT1G06590 APC5 4 AT3G28730 ATHMG (HIGH MOBILITY GROUP, STRUCTURE-SPECIFIC 4 RECOGNITION PROTEIN 1); TRANSCRIPTION FACTOR AT3G53230 CDC48, putative 4 AT3G01610 CDC48C|AAA-TYPE ATPASE FAMILY PROTEIN, CONTAINS PFAM 4 DOMAIN, PF00004: ATPASE, AAA FAMILY (‘A’TPASES ‘A’SSOCIATED WITH DIVERSE CELLULAR ‘A’CTIVITIES)| CHR3: 231658-235196 FORWARD|ALIASES: EMB1354, EMBRYO DEFECTIVE 1354, F4P135, F4P13_15 AT1G18040 CDKD; 3 4 AT5G03340 CELL DIVISION CONTROL PROTEIN 48 HOMOLOG E; ATPASE 4 AT5G11300 CYCA2; 2 4 AT1G15570 CYCA2; 3 4 AT1G80370 CYCA2; 4 4 AT2G26760 CYCB1; 4 4 AT2G17620 CYCB2; 1 4 AT4G35620 CYCB2; 2 4 AT3G50070 CYCD3; 3 4 AT3G05330 cyclin family low similarity to microtubule-binding protein TANGLED1 4 AT5G05490 DIF1/SYN1 4 AT1G69770 DNA (cytosine-5)-methyltransferase CMt3; Chromomethylase 3; 4 Protein CHROMOMETHYLASE3 AT4G02460 DNA mismatch repair protein 4 AT1G67320 DNA primase, large subunit family, contains Pfam profile PF04104: 4 Eukaryotic-type DNA primase, large subunit; similar to DNA primase large subunit (EC 2.7.7.—) (DNA primase 58 kDa subunit) (p58) (Swiss-Prot: P49643) (Homo sapiens) AT4G31210 DNA topoisomerase family protein, similar to DNA Topoisomerase I 4 (SP: Q9X3X7) {Zymomonas mobilis} AT5G63920 DNA topoisomerase III 4 AT5G06110 DNAJ heat shock N-terminal domain-containing protein/cell division 4 protein-related, similar to GlsA (Volvox carteri f. nagariensis) GI: 4633129; contains Pfam profiles PF00226 DnaJ domain, PF00249 Myb-like DNA-binding domain AT1G78650 expressed protein, weak similarity to DNA polymerase delta subunit 3 4 (DNA polymerase delta subunit p66) (Swiss-Prot: Q15054) (Homo sapiens) AT2G13330 F14O4.9 4 AT2G23430 KRP1 4 AT2G20980 MCM10 4 AT2G29570 PCNA2 4 AT4G14150 phragmoplast-associated kinesin-related protein (PAKRP1) 4 AT3G23670 phragmoplast-associated kinesin-related protein, putative, similar to 4 kinesin-like protein GB: CAB10194 from (Arabidopsis thaliana) AT5G58720 PRLI-INTERACTING FACTOR, PUTATIVE 4 AT1G53710 PROTEIN SERINE/THREONINE PHOSPHATASE 4 AT3G02920 replication protein-related, similar to replication protein A 30 kDa (Oryza 4 sativa (japonica cultivar-group)) GI: 13516746; contains InterPro entry IPR004365: OB-fold nucleic acid binding domain AT4G22970 similar to hypothetical protein [Arabidopsis thaliana] 4 (TAIR: At5g28550.1); similar to BIMB_EMENI CELL DIVISION-ASSOCIATED PROTEIN BIMB [Aspergillus nidulans FGSC A4] (GB: EAA60576.1); similar to probable spindle pole body component bimB - Emericella nidula AT5G61460 SMC-like protein 4 AT1G65660 SMP1 (SWELLMAP 1); NUCLEIC ACID BINDING 4 AT5G62000 transcriptional factor B3 family protein/auxin-responsive factor 4 AT5G16750 transducin family protein/WD-40 repeat family protein contains 8 4 WD-40 repeats (PF00400); similar to transducin homolog sazD - Homo sapiens, EMBL: U02609 AT2G14400 transposable element gene 4 AT2G42260 UVI4 4 AT1G57820 VARIANT IN METHYLATION 1 4 AT3G02820 zinc knuckle (CCHC-type) family protein, contains Pfam domain, 4 PF00098: Zinc knuckle AT5G22010 AAA-TYPE ATPASE FAMILY PROTEIN/BRCT 3 DOMAIN-CONTAINING PROTEIN AT2G14120 ADL2b 3 AT5G57160 ATLIG4 (ARABIDOPSIS THALIANA DNA LIGASE IV) 3 AT5G45720 ATP BINDING/DNA-DIRECTED DNA POLYMERASE/ 3 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING AT1G66730 ATP DEPENDENT DNA LIGASE FAMILY PROTEIN 3 AT2G32590 barren family protein, low similarity to SP: Q9Y7R3 Condensin complex 3 subunit 2 (p105) {Schizosaccharomyces pombe}; contains Pfam profile PF05786: Barren protein AT3G19590 BUB3-like2 3 AT4G22910 CCS52A1 3 AT4G11920 CCS52A2 3 AT4G33270 cdc20-1 3 AT3G25100 CDC45 (Cell division cycle 45)-like protein; Putative cell division cycle 3 protein 45 AT3G09840 CDC48 3 AT1G20930 CDKB2; 2 3 AT1G73690 CDKD; 1 3 AT4G28980 CDKF; 1 3 AT2G32900 centromere/kinetochore protein, putative (ZW10) 3 AT5G62410 Chromosome assembly protein homolog 3 AT1G44110 CYCA1; 1 3 AT1G47210 CYCA3; 2 3 AT4G37490 CYCB1; 1 3 AT1G76310 CYCB2; 4 3 AT4G34160 CYCD3; 1 3 AT4G34090 CYL1 3 AT3G20550 DDL (DAWDLE) 3 AT5G14960 DEL2 3 AT4G09140 DNA mismatch repair protein MLH1 3 AT3G18524 DNA mismatch repair protein MSH2 (MSH2) identical to SP|O24617 3 DNA mismatch repair protein MSH2 (AtMsh2) {Arabidopsis thaliana} AT4G02070 DNA mismatch repair protein MSH6-1 (MSH6-1) (AGAA.3) 3 AT5G55300 DNA topoisomerase I 3 AT3G17830 DNAJ HEAT SHOCK FAMILY PROTEIN 3 AT1G80030 DNAJ HEAT SHOCK PROTEIN, PUTATIVE 3 AT1G08840 EMB2411|DNA REPLICATION HELICASE, PUTATIVE, SIMILAR TO 3 HELICASE (XENOPUS LAEVIS) GI: 18845092: GB: AAL79550| CHR1: 2829582-2838372 REVERSE|ALIASES: EMB2411, EMBRYO DEFECTIVE 2411, F7G19.26 AT4G37120 expressed protein 3 AT5G58870 FTSH9 (FTSH PROTEASE 9); ATP-DEPENDENT PEPTIDASE/ 3 ATPASE/METALLOPEPTIDASE AT1G13980 GN (GNOM) 3 AT5G24330 Histone-lysine N-methyltransferase AtXR6; Protein SET DOMAIN 3 GROUP 34; trithorax-related protein 6; tRX-related protein 6 AT5G06830 IDENTICAL TO CDK5RAP3-LIKE PROTEIN [ARABIDOPSIS 3 THALIANA] (GB: Q9FG23); SIMILAR TO OS06G0320100 [ORYZA SATIVA (JAPONICA CULTIVAR-GROUP)] (GB: NP_001057510.1); SIMILAR TO CDK5 REGULATORY SUBUNIT ASSOCIATED PROTEIN 3 [MUS MUSCULUS] (GB: NP_084524.1); CONTAINS INTERPRO DOMAIN PROTEIN OF UNKNOWN FUNCTION DUF773; (INTERPRO: IPR008491) AT1G49620 KRP7 3 AT1G71830 leucine-rich repeat family protein/protein kinase family protein, 3 contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain AT1G80080 leucine-rich repeat family protein, contains leucine rich-repeat domains 3 Pfam: PF00560, INTERPRO: IPR001611; contains some similarity to Hcr2-5D (Lycopersicon esculentum) gi: 3894393: gb: AAC78596 AT3G25980 MAD2-like 3 AT5G51600 MAP65-3 3 AT1G44900 MCM2 3 AT2G16440 MCM4 3 AT2G07690 MCM5 3 AT5G54260 MRE11|DNA REPAIR AND MEIOSIS PROTEIN (MRE11), 3 IDENTICAL TO DNA REPAIR AND MEIOSIS PROTEIN (MRE11) GI: 5524769 FROM (ARABIDOPSIS THALIANA)| CHR5: 22049295-22055217 FORWARD|ALIASES: MDK4.8, MDK4_8 AT5G58230 MSI1 (MULTICOPY SUPRESSOR OF IRA1) 3 AT1G61000 Nuf2 family protein contains Pfam PF03800: Nuf2 family 3 domain/kinetochore protein NUF2 AT5G16690 ORC3 3 AT1G72150 PATL1 (PATELLIN 1); TRANSPORTER 3 AT1G50840 poll-like DNA polymerase, putative, similar to Poll-like DNA 3 polymerase (Oryza sativa) GI: 19912795 contains Pfam profiles PF01612: 3′-5′ exonuclease, PF00476: DNA polymerase I family A AT1G80190 PSF1 (GINS complex DNA replication) 3 AT2G45280 putative RAD51C-like DNA repair protein; supported by cDNA: 3 gi_15425730_dbj_AB062456.1_AB062456 AT2G31970 RAD50|DNA REPAIR-RECOMBINATION PROTEIN (RAD50), 3 IDENTICAL TO DNA REPAIR-RECOMBINATION PROTEIN GI: 7110148 FROM (ARABIDOPSIS THALIANA)| CHR2: 13607589-13616146 FORWARD|ALIASES: ATRAD50, DNA REPAIR RECOMBINATION PROTEIN, F22D22.28, F22D22_28 AT5G08020 Replication factor A-like protein 3 AT2G21790 Ribonucleoside-diphosphate reductase large subunit; AtRNR1; 3 Ribonucleoside-diphosphate reductase R1 subunit AT3G27060 ribonucleoside-diphosphate reductase small chain, putative/ 3 ribonucleotide reductase, putative, similar to ribonucleotide reductase R2 (Nicotiana tabacum) GI: 1044912; contains Pfam profile PF00268: Ribonucleotide reductase, small chain AT2G24490 RPA2 3 AT4G18590 RPA3 3 AT1G30690 SEC14 cytosolic factor family protein/phosphoglyceride transfer family 3 protein, contains Pfam PF00650: CRAL/TRIO domain; contains Pfam PF03765: CRAL/TRIO, N-terminus; similar to cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer prot AT1G74560 similar to nucleosome assembly protein (NAP) family protein 3 [Arabidopsis thaliana] (TAIR: At1g18800.1); similar to nucleosome/chromatin assembly factor A [Zea mays] (GB: AAK67146.1); contains InterPro domain Nucleosome assembly protein (NAP) (InterPro: IPR00 AT5G04320 similar to unknown protein [Arabidopsis thaliana] (TAIR: AT3G10440.1); 3 similar to hypothetical protein Osl_009118 [Oryza sativa (indica cultivar-group)] (GB: EAY87885.1); contains InterPro domain Shugoshin, C-terminal; (InterPro: IPR011515) AT5G49010 SLD5 (DNA replication) 3 AT5G51330 SWI1 (SWITCH1); PHOSPHOLIPASE C 3 AT4G02110 TOPBP1 3 AT2G01550 transposable element gene 3 AT2G15410 transposable element gene 3 AT4G33790 ACYL COA REDUCTASE, PUTATIVE 2 AT5G22420 ACYL COA REDUCTASE, PUTATIVE 2 AT4G16420 ADA2B (PROPORZ1); DNA BINDING/TRANSCRIPTION FACTOR 2 AT1G78580 alpha, alpha-trehalose-phosphate synthase, UDP-forming, putative 2 (Fragment) AT1G54960 ANP2 (ARABIDOPSIS NPK1-RELATED PROTEIN KINASE 2); 2 KINASE AT4G37750 ANT 2 AT1G78770 APC6 2 AT2G39090 APC7 2 AT3G48150 APC8 2 AT4G30080 ARF16 (AUXIN RESPONSE FACTOR 16); MIRNA BINDING/ 2 TRANSCRIPTION FACTOR AT1G50240 armadillo/beta-catenin repeat family protein, contains Pfam profile: 2 PF00514 armadillo/beta-catenin-like repeat AT1G67370 ASY1 (ASYNAPTIC 1); DNA BINDING 2 AT3G12400 ATELC/ELC; ubiquitin binding 2 AT3G52115 ATGR1 (GAMMA RESPONSE 1) 2 AT5G55230 ATMAP65-1 (MICROTUBULE-ASSOCIATED PROTEINS 65-1); 2 MICROTUBULE BINDING AT3G27730 ATP-dependent DNA helicase, putative 2 AT5G40820 ATR 2 AT5G16850 ATTERT (TELOMERASE REVERSE TRANSCRIPTASE); 2 TELOMERIC TEMPLATE RNA REVERSE TRANSCRIPTASE AT4G00020 BRCA2A (BREAST CANCER 2 LIKE 2A, EMBRYO SAC 2 DEVELOPMENT ARREST 20, MATERNAL EFFECT EMBRYO ARREST 43) AT5G01630 BRCA2B_ATBRCA2(V)_BRCA2(V)_BRCA2B (breast cancer 2 like 2 2B) AT2G13680 CALS5 (CALLOSE SYNTHASE 5); 1,3-BETA-GLUCAN SYNTHASE 2 AT2G20000 cdc27b 2 AT2G03670 CDC48B; ATPASE 2 AT1G76540 CDKB2; 1 2 AT5G64960 CDKC; 2 2 AT5G63370 CDKG; 1 2 AT3G02450 CELL DIVISION PROTEIN FTSH, PUTATIVE 2 AT5G55280 cell division protein FtsZ, chloroplast, putative 2 AT5G37630 chromosome condensation family protein, contains pfam profile: 2 PF04154 chromosome condensation protein 3, C-terminal region AT1G09600 CKL11 2 AT4G22940 CKL4 2 AT5G44290 CKL5 2 AT1G03740 CKL6 2 AT1G54610 CKL9 2 AT2G27970 CKS2 2 AT5G40840 cohesion family protein SYN2 (SYN2) 2 AT4G02570 cullin family protein NCBI Chain C, Crystal Structure Of the 2 Ddb1-Cul4a-Rbx1-Sv5v Complex AT1G26830 cullin3a 2 AT5G06150 CYCB1; 2 2 AT1G34460 CYCB1; 5 2 AT5G48640 CYCC1; 1 2 AT2G26430 CYCL1 2 AT4G19560 CYCT1; 2 2 AT5G45190 CYCT1; 5 2 AT3G01330 DEL3 2 AT4G35520 DNA mismatch repair family protein 2 AT1G65070 DNA MISMATCH REPAIR MUTS FAMILY PROTEIN 2 AT1G67630 DNA polymerase alpha subunit B family, contains Pfam profile: 2 PF04058 DNA polymerase alpha subunit B AT1G09815 DNA polymerase delta subunit 4 family, contains similarity to 2 Swiss-Prot: Q9HCU8 DNA polymerase delta subunit 4 (DNA polymerase delta subunit p12) (Homo sapiens) AT5G64420 DNA polymerase V family, contains Pfam domain PF04931: DNA 2 polymerase V AT1G14460 DNA polymerase-related, weak similarity to DNA polymerase III 2 holoenzyme tau subunit (Thermus thermophilus) GI: 2583049 AT5G55310 DNA topoisomerase I, putative 2 AT5G44610 DREPP PLASMA MEMBRANE POLYPEPTIDE-RELATED 2 AT2G36010 E2Fa 2 AT3G11220 ELP4 2 AT4G32700 Encodes a homolog of Drosophila MUS308 and mammalian DNA 2 polymerase, which prevent spontaneous or DNA damage-induced production of DNA double strand breaks. AT5G64630 Encodes the second largest subunit of the chromatin assembly 2 factor-1. Involved in organization of the shoot and root apical meristems. AT4G24790 expressed protein; expression supported by MPSS 2 AT3G24495 Expressed protein; GC donor splice site at exon 11; supported by 2 cDNA: gi_6224916_gb_AF193018.1_AF193018 AT4G23940 FTSH PROTEASE, PUTATIVE 2 AT5G01230 FtsJ-like methyltransferase family protein, contains Pfam profile: 2 PF01728 FtsJ-like methyltransferase AT1G48270 GCR1 (G-PROTEIN-COUPLED RECEPTOR 1) 2 AT1G10270 GRP23 (GLUTAMINE-RICH PROTEIN23); BINDING 2 AT2G26890 GRV2 (KATAMARI2); binding/heat shock protein binding 2 AT4G32880 homeobox-leucine zipper transcription factor (HB-8), identical to 2 HD-zip transcription factor (athb-8) (GI: 7270235) (Arabidopsis thaliana) AT5G46920 intron maturase, type II family protein 2 AT5G54670 kinesin-like protein C (KATC) 2 AT3G19150 KRP6 2 AT5G44635 MCM6 2 AT4G02060 MCM7 2 AT3G09660 MCM8 2 AT2G14050 MCM9 2 AT1G77320 MEI1 (MEIOSIS DEFECTIVE 1); TRANSCRIPTION COACTIVATOR 2 AT3G22880 meiotic recombination protein, putative 2 AT5G50110 METHYLTRANSFERASE-RELATED 2 AT5G24020 MIND (ACCUMULATION AND REPLICATION OF CHLOROPLAST 2 11) AT3G24320 mismatch binding protein, putative; similar to mismatch binding protein 2 Mus3 GB: AAF35250 from (Zea mays) AT5G49880 MITOTIC CHECKPOINT FAMILY PROTEIN 2 AT2G35630 MOR1|MICROTUBULE ORGANIZATION 1 PROTEIN (MOR1), 2 IDENTICAL TO MICROTUBULE ORGANIZATION 1 PROTEIN GI: 14317953 FROM (ARABIDOPSIS THALIANA)| CHR2: 14973757-14987661 FORWARD|ALIASES: GEM1, MICROTUBULE ORGANIZATION 1, T20F21.17, T20F21_17 AT4G17380 MSH4, similar to DNA mismatch repair protein MSH2 2 AT1G63680 Mur ligase family protein, contains Pfam profile: PF01225 Mur ligase 2 family, catalytic domain AT5G11510 MYB 3R4 2 AT3G02680 NBS1 (NIJMEGEN BREAKAGE SYNDROME 1) 2 AT3G57060 non-SMC condensin subunit, XCAP-D2/Cnd1 family protein, similar to 2 13S condensin XCAP-D2 subunit (Xenopus laevis) GI: 3764087; contains Pfam profile PF04594: Non-SMC condensin subunit, XCAP-D2/Cnd1 AT4G14700 ORC1A 2 AT4G29910 ORC5 2 AT4G30825 pentatricopeptide (PPR) repeat-containing protein, contains Pfam 2 profile PF01535: PPR repeat AT5G14520 pescadillo-related 2 AT2G13840 PHP DOMAIN-CONTAINING PROTEIN 2 AT3G63120 PLP1; 1 2 AT1G50230 protein kinase family protein, contains protein kinase domain, 2 Pfam: PF00069 AT3G63130 RAN GTPase activating protein 1 (RanGAP1), contains Pfam 2 PF00560: Leucine Rich Repeat domains; identical to RAN GTPase activating protein 1 (GI: 6708466)(Arabidopsis thaliana) AT1G16590 REV7 (REVERSIONLESS 7); DNA BINDING 2 AT5G27740 RFC3 2 AT1G21690 RFC4 2 AT1G77470 RFC5 2 AT1G48380 RHL1 (ROOT HAIRLESS 1) 2 AT4G33495 RPD1 (ROOT PRIMORDIUM DEFECTIVE 1) 2 AT5G35770 SAP (STERILE APETALA); TRANSCRIPTION FACTOR 2 AT1G72160 SEC14 CYTOSOLIC FACTOR FAMILY PROTEIN/ 2 PHOSPHOGLYCERIDE TRANSFER FAMILY PROTEIN AT4G09160 SEC14 CYTOSOLIC FACTOR FAMILY PROTEIN/ 2 PHOSPHOGLYCERIDE TRANSFER FAMILY PROTEIN AT3G51670 SEC14 cytosolic factor family protein/phosphoglyceride transfer family 2 protein, similar to polyphosphoinositide binding protein Ssh2p (GI: 2739046) {Glycine max};; contains Pfam PF00650: CRAL/TRIO domain; contains Pfam PF03765: CRAL/TRIO, N-terminus AT5G03730 SERINE/THREONINE-PROTEIN KINASE CTR1 2 AT4G14180 SIMILAR TO OS04G0347800 [ORYZA SATIVA (JAPONICA 2 CULTIVAR-GROUP)] (GB: NP_001052517.1); SIMILAR TO OSIGBA0130K07.4 [ORYZA SATIVA (INDICA CULTIVAR-GROUP)] (GB: CAH66368.1); SIMILAR TO OSJNBA0020I02.9 [ORYZA SATIVA (JAPONICA CULTIVAR-GROUP)] (GB: CAE02100.2); CONTAINS DOMAIN ARM REPEAT (SSF48371) AT1G08260 SIMILAR TO POL2A. DNA POLYMERASE EPSILON CATALYTIC 2 SUBUNIT. ESSENTIAL FOR ARABIDOPSIS GROWTH. NULL HOMOZYGOTES ARE EMBRYO LETHAL. PARTIAL LOSS OF FUNCTION ALLELES SHOW EMBRYO PATTERNING DEFECTS SUCH AS ROOT POLE DISPLACEMENT. DELAYED PROGRESSION THROUGH CELL CYCLE RESULTS IN EMBRYOS WITH SMALLER NUMBERS OF LARGER CELLS. AT2G27170 similar to SMC2-like condensin, putative (SMC2) (TITAN3) 2 AT5G24630 SIMILAR TO UNKNOWN PROTEIN [ARABIDOPSIS THALIANA] 2 (TAIR: AT2G22795.1); SIMILAR TO UNKNOWN PROTEIN [ORYZA SATIVA (JAPONICA CULTIVAR-GROUP)] (GB: BAD13052.1); SIMILAR TO OS02G0147700 [ORYZA SATIVA (JAPONICA CULTIVAR-GROUP)] (GB: NP_001045886.1) AT3G10440 SIMILAR TO UNKNOWN PROTEIN [ARABIDOPSIS THALIANA] 2 (TAIR: AT5G04320 AT3G17590 SNF5 homolog BSH (bsh) mRNA, complete cds 2 AT1G49040 stomatal cytokinesis defective/SCD1 protein (SCD1) 2 AT5G15920 structural maintenance of chromosomes (SMC) family protein (MSS2), 2 similar to SMC-related protein MSS2 (Arabidopsis thaliana) GI: 9965743 AT1G04110 subtilase family protein, contains similarity to subtilisin-like protease 2 gI: 3687307 AT3G04740 SWP (STRUWWELPETER) 2 AT1G08560 syntaxin-related protein KNOLLE 2 AT3G62980 TIR1 (TRANSPORT INHIBITOR RESPONSE 1); ubiquitin-protein 2 ligase AT1G30660 toprim domain-containing protein 2 AT1G30680 TOPRIM DOMAIN-CONTAINING PROTEIN 2 AT4G10710 transcriptional regulator-related 2 AT3G44540 TRANSDUCIN FAMILY PROTEIN/WD-40 REPEAT FAMILY 2 PROTEIN, CONTAINS 6 (4 SIGNIFICANT) WD-40 REPEATS (PF0400 AT2G15380 transposable element gene 2 AT2G15540 transposable element gene 2 AT2G18820 transposable element gene 2 AT2G28980 transposable element gene 2 AT4G04000 transposable element gene 2 AT3G54670 TTN8|SIMILAR TO STRUCTURAL MAINTENANCE OF 2 CHROMOSOMES (SMC) FAMILY PROTEIN [ARABIDOPSIS THALIANA] (TAIR: AT5G48600.1 AT3G20060 UBC19 (UBIQUITIN-CONJUGATING ENZYME 19); UBIQUITIN- 2 PROTEIN LIGASE AT1G50490 UBC20 2 AT1G02970 WEE1 2 AT5G08290 YLS8 (yellow-leaf-specific gene 8); catalytic 2 AT4G02980 ABP1 (ENDOPLASMIC RETICULUM AUXIN BINDING PROTEIN 1) 1 AT5G22500 ACYL COA REDUCTASE, PUTATIVE/MALE-STERILITY PROTEIN, 1 PUTATIVE AT1G14830 ADL1C/ADL5 (DYNAMIN-LIKE PROTEIN 5); GTP binding/GTPase 1 AT4G33650 ADL2a 1 AT5G61960 AML1 (ARABIDOPSIS MEI2-LIKE PROTEIN 1); RNA binding 1 AT4G01540 ANAC068/NTM1 (NAC WITH TRANSMEMBRANE MOTIF1); 1 TRANSCRIPTION FACTOR/TRANSCRIPTIONAL ACTIVATOR AT2G18290 APC10 1 AT2G04660 APC2 1 AT4G21530 APC4 1 AT3G54710 ATCDT1B/CDT1/CDT1B (ARABIDOPSIS HOMOLOG OF YEAST 1 CDT1 B); CYCLIN-DEPENDENT PROTEIN KINASE AT2G20190 ATCLASP/CLASP; binding AT4G18820 ATP BINDING/DNA-DIRECTED DNA POLYMERASE/ 1 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING AT4G21800 ATP-binding family protein 1 AT3G49780 ATPSK3|PHYTOSULFOKINES 3 (PSK3), IDENTICAL TO 1 PHYTOSULFOKINES 3 (PSK3) SP: Q9M2Y0 FROM (ARABIDOPSIS THALIANA)|CHR3: 18476664-18477361 FORWARD|ALIASES: PHYTOSULFOKINE 3 PRECURSOR, T16K530 AT1G58470 ATRBP1 (ARABIDOPSIS THALIANA RNA-BINDING PROTEIN 1); 1 RNA binding AT4G00100 ATRPS13A (RIBOSOMAL PROTEIN S13A); structural constituent of 1 ribosome AT3G20780 ATTOP6B (BRASSINOSTEROID INSENSITIVE 3, ROOT HAIRLESS 1 3) AT2G28350 auxin-responsive factor (ARF10) 1 AT1G69400 BUB3-like1 1 AT5G27080 cdc20-3 1 AT5G03455 cdc25 1 AT2G38620 CDKB1; 2 1 AT5G10270 CDKC; 1 1 AT1G66750 CDKD; 2 1 AT5G63610 CDKE; 1 1 AT1G67580 CDKG; 2 1 AT2G46520 CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN, PUTATIVE/ 1 IMPORTIN-ALPHA RE-EXPORTER, PUTATIVE AT2G25170 chromatin remodeling factor CHD3 (PICKLE) 1 AT2G26280 CID7; ATP BINDING/DAMAGED DNA BINDING 1 AT5G39420 CKL1 1 AT1G57700 CKL10 1 AT1G71530 CKL12 1 AT4G10010 CKL13 1 AT1G33770 CKL14 1 AT1G74330 CKL2 1 AT5G50860 CKL7 1 AT2G27960 CKS1 1 AT1G02980 cullin family protein, similar to cullin 1 (Homo sapiens) GI: 3139077; 1 contains Pfam profile PF00888: Cullin family AT1G69670 cullin3b 1 AT5G46210 cullin4 1 AT1G47220 CYCA3; 3 1 AT1G47230 CYCA3; 4 1 AT1G20590 CYCB2; 5 1 AT1G16330 CYCB3; 1 1 AT2G22490 CYCD2; 1 1 AT5G67260 CYCD3; 2 1 AT5G65420 CYCD4; 1 1 AT4G03270 CYCD6; 1 1 AT5G27620 CYCH; 1 1 AT3G21870 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 1 (TRYPANOSOMA BRUCEI) GI: 7339572, CYCLIN 6 (TRYPANOSOMA CRUZI) GI: 12005317; CONTAINS PFAM PROFILE PF00134: CYCLIN, N-TERMINAL DOMAIN|CHR3: 7703878-7704836 REVERSE|ALIASES: MEK6.1 AT5G50375 cyclopropyl isomerase (CPI1) 1 AT2G45080 CYCP3; 1 (CYCLIN P3; 1); CYCLIN-DEPENDENT PROTEIN KINASE 1 AT3G60550 CYCP3; 2 1 AT5G61650 CYCP4; 2|CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 1 (TRYPANOSOMA BRUCEI) GI: 7339572, CYCLIN 6 (TRYPANOSOMA CRUZI) GI: 12005317; CONTAINS PFAM PROFILE PF00134: CYCLIN, N-TERMINAL DOMAIN|CHR5: 24795491-24796245 FORWARD|ALIASES: CYCP4, K11J9.17, K11J9_17 AT1G35440 CYCT1; 1 1 AT1G27630 CYCT1; 3 1 AT4G19600 CYCT1; 4 1 AT1G01040 DEAD/DEAH box helicase carpel factory/CAF 1 AT3G48160 DEL1 1 AT5G54090 DNA mismatch repair MutS family protein 1 AT2G42120 DNA polymerase delta small subunit 1 AT1G10520 DNA polymerase lambda (POLL) 1 AT2G32000 DNA TOPOISOMERASE FAMILY PROTEIN 1 AT5G63960 DNA-directed DNA polymerase delta catalytic subunit, putative 1 (POLD1) AT2G27120 DNA-directed DNA polymerase epsilon catalytic subunit, putative, 1 similar to SP|Q07864 DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A) {Homo sapiens}; contains Pfam profiles: PF03175 DNA polymerase type B, organellar AT2G22360 DNAJ heat shock family protein 1 AT3G60190 dynamin-like protein E 1 AT5G13680 ELO2 1 AT1G12360 ENCODES A SEC1 PROTEIN AND EXPRESSED THROUGHOUT 1 THE PLANT. PHYSICALLY INTERACTS WITH SYNTAXIN1 AND IS REQUIRED FOR CYTOKINESIS. AT3G23580 ENCODES ONE OF THE 3 RIBONUCLEOTIDE REDUCTASE (RNR) 1 SMALL SUBUNIT GENES (RNR2A). FUNCTIONALLY REDUNDANT WITH THE RIBONUCLEOTIDE REDUCTASE TSO2. MRNA WAS SHOWN TO SPECIFICALLY ACCUMULATE DURING THE S-PHASE OF THE CELL CYCLE IN SYNCHRONIZED TOBACCO BY2 CELLS. CRITICAL FOR CELL CYCLE PROGRESSION. DNA DAMAGE REPAIR AND PLANT DEVELOPMENT. AT1G50250 FTSH1 (FTSH PROTEASE 1); ATP-DEPENDENT PEPTIDASE/ 1 ATPASE/METALLOPEPTIDASE AT5G53170 FTSH11 (FTSH PROTEASE 11); ATP-DEPENDENT PEPTIDASE/ 1 ATPASE/METALLOPEPTIDASE AT2G36250 FTSZ2-1 (FTSZ HOMOLOG 2-1); STRUCTURAL MOLECULE 1 AT3G52750 FTSZ2-2 (FtsZ2-2); structural molecule 1 AT2G22475 GRAM DOMAIN-CONTAINING PROTEIN/ABA-RESPONSIVE 1 PROTEIN-RELATED ATMG01250 HYPOTHETICAL PROTEIN 1 AT5G08550 ILP1 (INCREASED LEVEL OF POLYPLOIDY1-1D); TRANSLATION 1 REPRESSOR AT1G30010 INTRON MATURASE, TYPE II FAMILY PROTEIN 1 AT4G21270 kinesin-like protein A (KATA) 1 AT5G35520 kinetochore protein-related 1 AT3G50630 KRP2 1 AT5G48820 KRP3 1 AT2G32710 KRP4 1 AT3G24810 KRP5 1 AT2G26330 leucine-rich repeat protein kinase, putative (ERECtA), identical to 1 uncharacterized receptor protein kinase ERECtA (Arabidopsis thaliana) gi: 1389566: dbj: BAA11869; contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: Protein kinase domain AT3G56700 MALE STERILITY PROTEIN, PUTATIVE 1 AT4G30820 MAT1 1 AT1G66170 MMD1 (MALE MEIOCYTE DEATH 1); DNA BINDING 1 AT4G20900 MS5 (MALE-STERILE 5) 1 AT1G79150 NOC3_DNA replication initiation 1 AT2G01840 non-LTR retrotransposon family (LINE), has a 9.6e−34 P-value blast 1 match to GB: NP_038607 L1 repeat, Tf subfamily, member 9 (LINE-element) (Mus musculus) AT2G35190 NPSN11 (NOVEL PLANT SNARE 11); protein transporter 1 AT1G77620 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING 1 AT4G12620 ORC1 1 AT3G44550 OXIDOREDUCTASE, ACTING ON THE CH-CH GROUP OF DONORS 1 AT3G44560 OXIDOREDUCTASE, ACTING ON THE CH-CH GROUP OF DONORS 1 AT5G10480 PAS2 (PASTICCINO 2) 1 AT1G07370 PCNA1 1 AT1G71440 PFI_TFC E_PFI (PFIFFERLING) 1 AT2G18040 PIN1 1 AT5G22130 PNT1 (PEANUT 1); MANNOSYLTRANSFERASE/TRANSFERASE, 1 TRANSFERRING GLYCOSYL GROUPS AT3G20540 POLGAMMA1 (POLYMERASE GAMMA 1); DNA BINDING/ 1 DNA-DIRECTED DNA POLYMERASE AT4G14713 PPD1 (PEAPOD 1) 1 AT1G49180 protein kinase family protein 1 AT3G12530 PSF2 (GINS complex DNA replication) 1 AT2G17910 putative non-LTR retroelement reverse transcriptase 1 AT4G36390 radical SAM domain-containing protein/TRAM domain-containing 1 protein AT1G63160 replication factor, putative; similar to GI: 4972952 from (Mus musculus) 1 (Mamm. Genome (2000) In press) AT5G45400 replication protein, putative, similar to replication protein A 70 kDa 1 (Oryza sativa (japonica cultivar-group)) GI: 13536993; contains InterPro entry IPR004365: OB-fold nucleic acid binding domain, PF04057: Replication factor-A protein 1, N-terminal domain AT4G19130 replication protein-related, similar to replication protein A 70 kDa (Oryza 1 sativa) GI: 13536993; contains Pfam profile PF00098: Zinc knuckle AT4G20520 RNA binding/RNA-directed DNA polymerase 1 AT2G20580 RPN1 1 AT3G54220 SCR (SCARECROW); TRANSCRIPTION FACTOR 1 AT1G14750 SDS 1 AT1G22530 SEC14 cytosolic factor family protein 1 AT1G34210 SERK2 (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2); 1 KINASE AT5G52800 SIMILAR TO PREDICTED: HYPOTHETICAL PROTEIN [RATTUS 1 NORVE (GB: XP_001060721.1); SIMILAR TO OS07G0467900 [ORYZA SATIVA (JAPONICA CULTIVAR-GR AT5G58650 SIMILAR TO UNKNOWN PROTEIN [ARABIDOPSIS THALIANA] 1 (TAIR: AT3G47295.1) AT1G75950 SKP1 (ARABIDOPSIS SKP1 HOMOLOGUE); ubiquitin-protein ligase 1 AT3G47460 SMC2-like condensin, putative/chromosome assembly protein 1 homolog; CHROMOSOME ASSEMBLY PROTEIN XCAP-E - Xenopus laevis, SWISSPROT: XCPE_XENLA AT2G02480 STI (STICHEL); ATP BINDING/DNA-DIRECTED DNA 1 POLYMERASE AT5G07660 structural maintenance of chromosomes (SMC) family protein 1 AT3G51770 tetratricopeptide repeat (TPR)-containing protein 1 AT5G23070 thymidine kinase, putative, similar to thymidine kinase (Oryza sativa) 1 SWISS-PROT: O81263 AT3G01780 TPLATE 1 AT4G07600 transposable element gene 1 AT4G09710 transposable element gene 1 AT4G14470 transposable element gene 1 AT4G04230 transposable element gene 1 AT3G18730 TSK (TONSOKU) 1 AT1G22275 unknown protein 1 AT5G42270 VAR1 (VARIEGATED 1); ATP-DEPENDENT PEPTIDASE/ATPASE/ 1 METALLOPEPTIDASE AT2G33880 WOX9 (STIMPY); transcription factor 1 AT1G24490 ALB4 (ALBINA 4) 0 AT5G28640 AN3 0 AT3G05870 APC11 0 AT2G37630 AS1/ATMYB91/ATPHAN/MYB91 (ASYMMETRIC LEAVES 1, MYB 0 DOMAIN PROTEIN 91); DNA binding/protein homodimerization/ transcription factor AT3G21850 ASK9 (ARABIDOPSIS SKP1-LIKE 9); ubiquitin-protein ligase 0 AT4G32200 ASY2; DNA binding 0 AT3G33520 ATARP6; structural constituent of cytoskeleton 0 AT3G48190 ataxia-telangiectasia mutated protein AtATM 0 AT5G05620 ATGCP2/TUBG2 (GAMMA-TUBULIN); structural molecule 0 AT3G20475 ATP binding/damaged DNA binding 0 AT1G49250 ATP dependent DNA ligase family protein 0 AT1G13590 ATPSK1 (PHYTOSULFOKINE 1 PRECURSOR); growth factor 0 AT2G22860 ATPSK2_ATPSK2 (PHYTOSULFOKINE 2 PRECURSOR); growth 0 factor AT5G65870 ATPSK5 (PHYTOSULFOKINE 5 PRECURSOR); growth factor 0 AT4G37720 ATPSK6 (PHYTOSULFOKINE 6 PRECURSOR); growth factor 0 AT1G14410 ATWHY1/PTAC1 (A. THALIANA WHIRLY 1); DNA binding/telomeric 0 DNA binding AT5G09790 ATXR5 (SETDOMAIN GROUP 15); DNA binding 0 AT3G24730 catalytic 0 AT3G48750 CDKA; 1 0 AT3G54180 CDKB1; 1 0 AT5G66130 cell cycle checkpoint protein-related, weak similarity to cell cycle 0 checkpoint protein RAD17 (Homo sapiens) GI: 4102916 Q94G54 Cell division control protein 6 0 Q9C8M6 Cell division control protein, putative; 15914-18846 0 Q9LFB3 Cell division-like protein 0 AT1G53050 CKL15 0 AT3G05050 CKL8 0 AT3G15170 CUC1 (CUP-SHAPED COTYLEDON1); transcription factor 0 AT1G20610 CYCB2; 3 0 AT5G48630 CYCC1; 2 0 AT5G10440 CYCD4; 2 0 AT5G02110 CYCD7; 1 0 AT2G01905 CYCJ18 0 Q38818 Cyclin 2 0 AT2G44740 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 0 (TRYPANOSOMA BRUCEI) GI: 7339572, CYCLIN 6 (TRYPANOSOMA CRUZI) GI: 12005317; CONTAINS PFAM PROFILE PF00134: CYCLIN, N-TERMINAL DOMAIN|CHR2: 18449064-18450471 REVERSE|ALIASES: F16B22.23 AT5G07450 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 0 (TRYPANOSOMA BRUCEI) GI: 7339572, CYCLIN 6 (TRYPANOSOMA CRUZI) GI: 12005317; CONTAINS PFAM PROFILE PF00134: CYCLIN, N-TERMINAL DOMAIN|CHR5: 2358353-2359309 REVERSE|ALIASES: T2I1.160, T2I1_160 AT1G22840 cytochrome c, putative 0 AT4G26701 DNA binding/DNA topoisomerase type I 0 AT3G15960 DNA mismatch repair MutS family protein 0 AT5G22110 DNA POLYMERASE EPSILON SUBUNIT B FAMILY, CONTAINS 0 PFAM PROFILE: PF04042 DNA POLYMERASE EPSILON SUBUNIT B|CHR5: 7330828-7334181 REVERSE|ALIASES: NONE AT5G64520 DNA repair protein-related 0 AT1G63990 DNA topoisomerase VIA, putative (SPO11-2) 0 AT4G39960 DNAJ heat shock family protein 0 AT5G62450 DOMINO1 0 AT5G03415 DPb 0 AT5G50320 ELO3 0 Q9FMR4 Emb|CAB92117.1 0 AT1G24590 ENCODES A MEMBER OF THE ERF (ETHYLENE RESPONSE 0 FACTOR) SUBFAMILY B-1 OF ERF/AP2 TRANSCRIPTION FACTOR FAMILY. THE PROTEIN CONTAINS ONE AP2 DOMAIN. THERE ARE 15 MEMBERS IN THIS SUBFAMILY INCLUDING ATERF-3. ATERF-4. ATERF-7. AND LEAFY PETIOLE. THIS GENE FUNCTIONS IN THE REGENERATION OF SHOOTS IN TISSUE CULTURE. PROBABLY THROUGH TRANSCRIPTIONAL REGULATION OF CUC1. MAY ALSO BE INVOLVED IN ACTIVATION OF THE CELL CYCLE VIA CYCD1; 1. AT5G26680 ENDONUCLEASE, PUTATIVE, SIMILAR TO SWISS-PROT: P39748 0 FLAP ENDONUCLEASE-1 (MATURATION FACTOR 1) (MF1) (HOMO SAPIENS)|CHR5: 9311885-9315478 REVERSE|ALIASES: NONE AT1G22260 expressed protein 0 Q9M874 F16B3.31 protein 0 Q9FX75 F19K19.10 protein 0 Q9FYF5 F1N21.20 0 O81303 F6N15.14 protein (Putative BRCA2 homolog) 0 AT2G14650 F9D12.11 protein (contains similarity to reverse transcriptases) 0 AT3G24140 FMA (FAMA); DNA binding/transcription activator/transcription factor 0 AT2G22942 growth factor 0 AT5G42080 GTP-binding protein/phragmoplastin, putative 0 AT1G47840 hexokinase, putative 0 AT5G03410 histidyl-tRNA synthetase - like protein 0 AT2G44950 HUB1 0 AT2G44960 HUB1 0 AT3G52630 hypothetical protein 0 AT1G74350 intron maturase, type II family protein 0 AT5G03150 JKD (JACKDAW); nucleic acid binding/protein binding/protein 0 homodimerization/transcription factor/zinc ion binding Q2V0Z5 Kinetochore protein 0 AT2G30410 KIS (KIESEL); unfolded protein binding 0 ATMG00520 MATR 0 AT5G22260 MS1 (MALE STERILITY 1); DNA binding 0 AT3G11980 MS2 (MALE STERILITY 2) 0 AT2G01120 ORC4 0 AT4G27650 PEL1 (PELOTA); translation release factor 0 AT2G01500 PFS2 (PRETTY FEW SEEDS 2); transcription factor 0 AT3G44735 PSK1 (PHYTOSULFOKINE 3 PRECURSOR); growth factor 0 Q9M8S3 Putative CCHC-type zinc finger protein 0 AT4G39920 putative protein 0 AT5G22370 putative protein; similar to unknown protein (emb|CAB92117.1) 0 AT2G07660 putative retroelement pol polyprotein 0 O80896 Putative uncharacterized protein At2g32590 0 Q9M013 Putative uncharacterized protein F7A7_150 0 O82745 Putative uncharacterized protein F7H19.150 (Putative uncharacterized 0 protein AT4g22970) Q9C953 Putative uncharacterized protein T7P1.14 0 AT4G20050 QRT3 (QUARTET 3) 0 AT2G06510 replication protein, putative similar to replication protein A 70 kDa 0 AT4G29090 reverse transcriptase, putative/RNA-dependent DNA polymerase, 0 putative AT2G25100 ribonuclease HII family protein 0 AT5G40942 RNR2B 0 AT2G36985 ROT4 (ROTUNDIFOLIA4) 0 AT4G18730 RPL16B (ribosomal protein L16B); structural constituent of ribosome 0 AT1G17235 RTFL11 (ROTUNDIFOLIA LIKE 11) 0 AT4G37650 SHR (SHORT ROOT); transcription factor 0 AT5G04470 SIM 0 AT3G55490 similar to TTN10 (TITAN 10) 0 AT5G62440 similar to unnamed protein product [Vitis vinifera] (GB: CAO64547.1) 0 Q9FGA0 Similarity to glucose inhibited division protein B 0 AT1G20330 SMT2 (STEROL METHYLTRANSFERASE 2) 0 AT4G27330 SPL (SPOROCYTELESS) 0 AT1G02065 SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8); DNA 0 binding AT3G07800 thymidine kinase, putative, similar to thymidine kinase (Oryza sativa) 0 SWISS-PROT: O81263 AT2G05610 transposable element gene 0 AT4G08830 transposable element gene 0 AT4G10580 transposable element gene 0 Q9FLP1 Trigger factor-like protein 0 AT1G19080 TTN10 (TITAN 10) 0 AT3G61650 TUBG1 (GAMMA-TUBULIN); STRUCTURAL MOLECULE 0 AT1G05560 UGT1 (UDP-glucosyl transferase 75B1); UDP-glycosyltransferase/ 0 transferase, transferring glycosyl groups AT1G47200 WPP2 (WPP domain protein 2) 0 AT5G57450 XRCC3|DNA REPAIR FAMILY PROTEIN, CONTAINS SIMILARITY 0 TO SWISS-PROT: O43542 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3) (HOMO SAPIENS)| CHR5: 23290319-23292202 REVERSE|ALIASES: ATXRCC3, MUA2.3, MUA2_3

TABLE 6 New candidate cell cycle proteins. Locus Description # of motifs Overview of 40 putative new cell cycle proteins identified in the core dataset containing at least two of the cell cycle-related features listed in Table S4. The number of identified features per protein is shown. AT2G44580 DCC1 6 AT3G57860 UVI4-like 5 AT4G38900 bZIP protein 5 AT1G32310 F27G20.14 5 AT4G17020 transcription factor-related 4 AT5G09900 EMB2107, RPN5A, MSA 4 AT5G40460 expressed 4 AT3G49240 EMB1796 4 AT2G17350 similar to hypothetical protein [Vitis vinifera] (GB: CAN62847.1) 4 AT5G24690 similar to RER1 (RETICULATA-RELATED 1) [Arabidopsis thaliana] 4 (TAIR: AT5G22790.1) AT4G25550 M7J2_80 4 AT3G15180 proteasome-related 3 AT2G36130 peptidyl-prolyl cis-trans isomerase, putative/cyclophilin, putative/rotamase 3 AT3G16060 kinesin motor family protein 3 AT3G10180 kinesin motor protein-related 3 AT5G65460 KCA2 3 AT5G05780 RPN8A, AE3, ATHMOV34 3 AT1G06070 bZIP transcription factor, putative (bZIP69) 3 AT1G71380 ATGH9B3, ATCEL3 3 AT3G05530 ATS6A.2, RPT5A 2 AT1G01880 DNA repair protein, putative 2 AT4G34150 C2 domain-containing protein 2 AT5G13030 similar to hypothetical protein Osl_021963 [Oryza sativa] (GB: EAZ00731.1) 2 AT4G14310 DL3195C 2 AT5G26360 chaperonin, putative 2 AT5G49510 VHL binding protein, putative/prefoldin, putative 2 AT3G20050 ATTCP-1 2 AT1G29150 RPN6, ATS9 2 AT3G15970 Ran-binding protein 1 domain-containing protein/RanBP1 domain-containing 2 protein AT4G28230 similar to unnamed protein product [Vitis vinifera] (GB: CAO41238.1) 2 AT5G23540 26S proteasome regulatory subunit, putative 2 AT5G41190 similar to hypothetical protein [Vitis vinifera] (GB: CAN66411.1) 2 AT2G03820 nonsense-mediated mRNA decay NMD3 family protein 2 AT1G20480 4-coumarate--CoA ligase family protein/4-coumaroyl-CoA synthase family 2 protein AT1G09270 importin alpha-1 subunit, putative (IMPA4) 2 AT1G23190 phosphoglucomutase, cytoplasmic, putative/glucose phosphomutase, putative 2 AT2G06990 HEN2 2 AT5G58290 RPT3 2 AT5G20920 EMB1401, EIF2 BETA 2 AT1G20200 EMB2719 2 Overview of 82 putative new cell cycle proteins identified in the non-core dataset containing at least two of the cell cycle-related features listed in Table S4. The number of identified features per protein is shown. AT5G18620 CHR17 6 AT4G38780 splicing factor, putative 5 AT1G01970 pentatricopeptide (PPR) repeat-containing protein 5 AT4G38900 bZIP protein 5 AT4G17020 transcription factor-related 4 AT2G46020 ATBRM, CHR2, BRM 4 AT5G10800 RNA recognition motif (RRM)-containing protein 4 AT5G40460 expressed 4 AT1G36160 AT-ACC1, EMB22, GK, PAS3, ACC1 4 AT1G77180 chromatin protein family 4 AT1G16520 similar to unknown protein [Arabidopsis thaliana] (TAIR: AT1G56080.1) 4 AT3G49240 EMB1796 4 AT4G24680 similar to unnamed protein product [Vitis vinifera] (GB: CAO64289.1) 4 AT2G25730 binding/heme binding 4 AT5G38480 RCI1, GRF3 4 AT4G25550 M7J2_80 4 AT3G05190 aminotransferase class IV family protein 4 AT4G35740 RecQI3 4 AT3G62240 zinc finger (C2H2 type) family protein 3 AT3G45970 EXPL1, ATEXPL1, ATHEXP BETA 2.1, ATEXLA1 3 AT3G56690 CIP111 3 AT3G56860 UBA2A 3 AT3G01280 porin, putative 3 AT3G20390 endoribonuclease L-PSP family protein 3 AT5G03740 HDT3, HD2C 3 AT5G25210 similar to unknown protein [Arabidopsis thaliana] (TAIR: AT4G32030.1) 3 AT1G48920 ATNUC-L1, PARL1 3 AT5G58150 leucine-rich repeat transmembrane protein kinase, putative 3 AT1G17340 phosphoinositide phosphatase family protein 3 AT1G23860 RSZP21, SRZ21, SRZ-21 3 AT2G16950 protein transporter 3 AT1G06070 bZIP transcription factor, putative (bZIP69) 3 AT1G71380 ATGH9B3, ATCEL3 3 AT2G44350 CSY4, ATCS 3 AT1G30860 protein binding/zinc ion binding 3 AT3G47930 ATGLDH 3 AT1G03060 WD-40 repeat family protein/beige-related 3 AT4G21860 MSRB2 3 AT2G30470 HSI2 2 AT1G80720 mitochondrial glycoprotein family protein/MAM33 family protein 2 AT1G09760 U2A′ 2 AT1G52360 coatomer protein complex, subunit beta 2 (beta prime), putative 2 AT1G22300 GF14 EPSILON, GRF10 2 AT3G13640 ATRLI1 2 AT5G12140 ATCYS1 2 AT1G66340 EIN1, ETR, ETR1 2 AT1G42440 similar to unknown protein [Arabidopsis thaliana] (TAIR: AT1G06720.1) 2 AT4G09320 NDPK1 2 AT5G54900 ATRBP45A 2 AT1G09100 RPT5B 2 AT1G52730 transducin family protein/WD-40 repeat family protein 2 AT3G49430 SRP34A 2 AT3G53880 aldo/keto reductase family protein 2 AT4G16630 DEAD/DEAH box helicase, putative (RH28) 2 AT2G03820 nonsense-mediated mRNA decay NMD3 family protein 2 AT1G23190 phosphoglucomutase, cytoplasmic, putative/glucose phosphomutase, 2 putative AT3G01540 ATDRH1, DRH1 2 AT5G20920 EMB1401, EIF2 BETA 2 AT4G14310 DL3195C 2 AT1G09430 ACLA-3 2 AT2G33340 transducin family protein/WD-40 repeat family protein 2 AT1G01880 DNA repair protein, putative 2 AT5G62350 invertase/pectin methylesterase inhibitor family protein/DC 1.2 homolog 2 (FL5-2I22) AT4G34150 C2 domain-containing protein 2 AT5G46780 VQ motif-containing protein 2 AT5G26360 chaperonin, putative 2 AT4G38440 similar to hypothetical protein [Vitis vinifera] (GB: CAN83259.1) 2 AT3G29800 AAA-type ATPase family 2 AT5G58290 RPT3 2 AT3G20050 ATTCP-1 2 AT1G19520 NFD5 2 AT4G26870 aspartyl-tRNA synthetase, putative/aspartate--tRNA ligase, putative 2 AT1G56080 similar to unknown protein [Arabidopsis thaliana] (TAIR: AT1G16520.1) 2 AT5G12380 annexin, putative 2 AT4G28230 similar to unnamed protein product [Vitis vinifera] (GB: CAO41238.1) 2 AT2G06210 VIP6, ELF8 2 ATCG00480 ATPB 2 AT5G02530 RNA and export factor-binding protein, putative 2 AT1G31760 SWIB complex BAF60b domain-containing protein 2 AT5G06680 ATSPC98, SPC98 2 AT2G16570 ATASE1, ATASE 2 AT1G62390 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein/ 2 tetratricopeptide repeat (TPR)-containing protein AT1G43800 acyl-(acyl-carrier-protein) desaturase, putative/stearoyl-ACP desaturase, 2 putative

TABLE 7 Overview of microarray experiments used to calculate the transcript PCCs. List of experiments used to build an Arabidopsis ATH1 micro-array compendium of 518 experiments focused on cell cycle or plant growth and development used to calculate the transcript Pearson correlation coefficients. Description Reference co-2; 3 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/co-3-1.CEL Col-0; 3 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Col-3-1.CEL ft-2; 3 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/ft-3-1.CEL Ler; 3 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Ler-3-1.CEL lfy-12; 3 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/lfy-3-1.CEL co-2; 5 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/co-5-1.CEL Col-0; 5 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Col-5-1.CEL ft-2; 5 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/ft-5-1.CEL Ler; 5 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Ler-5-1.CEL lfy-12; 5 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/lfy-5-1.CEL co-2; 7 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/co-7-1.CEL Col-0; 7 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Col-7-1.CEL ft-2; 7 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/ft-7-1.CEL Ler; 7 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/Ler-7-1.CEL lfy-12; 7 days long day condition; apical region; AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ rosette stage CEL/lfy-7-1.CEL co-2; no treatment; apical region; rosette stage AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ CEL/co-0-1.CEL Col-0; no treatment; apical region; rosette stage AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ CEL/Col-0-1.CEL ft-2; no treatment; apical region; rosette stage AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ CEL/ft-0-1.CEL Ler; no treatment; apical region; rosette stage AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ CEL/Ler-0-1.CEL lfy-12; no treatment; apical region; rosette stage AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ CEL/lfy-0-1.CEL Wt roots; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ CEL/ATGE_3_A. CEL Wt roots; 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ CEL/ATGE_9_A. CEL Wt root; 15 days long day (16/8) 1x MS agar, 1% AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ sucrose CEL/ATGE_93_A. CEL Wt root; 8 days continuous light 1x MS agar AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ CEL/ATGE_94_A. CEL Wt root; 8 days continuous light 1x MS agar, 1% sucrose AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ CEL/ATGE_95_A. CEL Wt root; 21 days continuous light 1x MS agar AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ CEL/ATGE_98_A. CEL Wt root; 21 days continuous light 1x MS agar, 1% AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ sucrose CEL/ATGE_99_A. CEL Wt seedling, green parts 21 days continuous light 1x MS AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ agar CEL/ATGE_100_A.CEL Wt seedling, green parts 21 days continuous light 1x MS AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ agar, 1% sucrose CEL/ATGE_101_A.CEL Wt developmental drift, entire rosette after transition AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/CEL/ to flowering, but before bolting 21 days continuous ATGE_22_A.CEL light soil Wt as above 22 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ CEL/ATGE_23_A.CEL Wt as above 23 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ CEL/ATGE_24_A.CEL Wt seedling, green parts; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ CEL/ATGE_7_A2.CEL Wt seedling, green parts 8 days continuous light 1x MS AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ agar CEL/ATGE_96_A.CEL Wt seedling, green parts 8 days continuous light 1x MS AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ agar, 1% sucrose CEL/ATGE_97_A.CEL Wt siliques, w/ seeds stage 3; mid globular to early AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ heart embryos 8 wk long day (16/8) soil CEL/ATGE_76_B.CEL Wt siliques, w/ seeds stage 4; early to late heart embryos AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 8 wk long day (16/8) soil CEL/ATGE_77_D.CEL Wt siliques, w/ seeds stage 5; late heart to mid torpedo AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ embryos 8 wk long day (16/8) soil CEL/ATGE_78_D.CEL Wt seeds, stage 6, w/o siliques; mid to late torpedo AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ embryos 8 wk long day (16/8) soil CEL/ATGE_79_A.CEL Wt seeds, stage 7, w/o siliques; late torpedo to early AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ walking-stick embryos 8 wk long day (16/8) soil CEL/ATGE_81_A.CEL Wt seeds, stage 8, w/o siliques; walking-stick to early AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ curled cotyledons CEL/ATGE_82_A.CEL Wt seeds, stage 9, w/o siliques; curled cotyledons to AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ early green cotyledons embryos; 8 wk long day CEL/ATGE_83_A.CEL (16/8) soil Wt seeds, stage 10, w/o siliques; green cotyledons AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ embryos 8 wk long day (16/8) soil CEL/ATGE_84_A.CEL Wt flowers stage 9, 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_31_A2.CEL Wt flowers stage 10/11, 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_32_A2.CEL Wt flowers stage 12, 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_33_A.CEL Wt flowers stage 12, sepals 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_34_A.CEL Wt flowers stage 12, petals 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_35_A.CEL Wt flowers stage 12, stamens 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_36_A.CEL Wt flowers stage 12, carpels 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_37_A.CEL Wt flowers stage 15, 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_39_A.CEL Wt flowers stage 15, pedicels 21+ days continuous AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ light soil CEL/ATGE_40_A.CEL Wt flowers stage 15, sepals 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_41_A.CEL Wt flowers stage 15, petals 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_42_B.CEL Wt flowers stage 15, stamen 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_43_A.CEL Wt flowers stage 15, carpels 21+ days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ soil CEL/ATGE_45_A.CEL Wt mature pollen 6 wk continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_73_A.CEL Wt flower 28 days long day (16/8) soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ CEL/ATGE_92_A.CEL clv3-7 flower stage 12; multi-carpel gynoeceum; enlarged AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ meristem; increased organ number; 21+ days continuous CEL/ATGE_53_A.CEL light soil lfy-12 flower stage 12; shoot characteristics; most organs AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ leaf-like 21+ days continuous light soil CEL/ATGE_54_A.CEL ap1-15 flower stage 12; sepals replaced by leaf-like AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ organs, petals mostly lacking, 2° flowers; 21+ days CEL/ATGE_55_A.CEL continuous light soil ap2-6 flower stage 12; no sepals or petals 21+ days AtGen Express; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ continuous light soil CEL/ATGE_56_A.CEL ap3-6 flower stage 12; no petals or stamens 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ continuous light soil CEL/ATGE_57_A.CEL ag-12 flower stage 12; no stamens or carpels 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ continuous light soil CEL/ATGE_58_A.CEL ufo-1 flower stage 12; filamentous organs in whorls two AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ and three 21+ days continuous light soil CEL/ATGE_59_A.CEL Wt cotyledons; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_1_A.CEL Wt rosette leaf #4, 1 cm long 10 days continuous light AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ soil CEL/ATGE_10_A.CEL gl1-T rosette leaf #4, 1 cm long 10 days continuous AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ light soil CEL/ATGE_11_A.CEL Wt rosette leaf #2, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_12_A.CEL Wt rosette leaf #4, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_13_A.CEL Wt rosette leaf #6, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_14_A.CEL Wt rosette leaf #8, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_15_A.CEL Wt rosette leaf #10, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_16_A.CEL Wt rosette leaf #12, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_17_A.CEL gl1-T rosette leaf #12, 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_18_A.CEL Wt leaf 7, petiole 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_19_A.CEL Wt leaf 7, proximal half 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_20_A.CEL Wt leaf 7, distal half 17 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_21_A.CEL Wt senescing leaves 35 days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_25_A.CEL Wt cauline leaves 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_26_A.CEL Wt leaves 1 + 2; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_5_A.CEL Wt vegetative rosette 7 days short day (10/14) soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_87_A.CEL Wt vegetative rosette 14 days short day (10/14) soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_89_A.CEL Wt vegetative rosette 21 days short day (10/14) soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_90_A.CEL Wt leaf 15 days long day (16/8) 1x MS agar, 1% sucrose AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ CEL/ATGE_91_A.CEL Wt hypocotyl; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ CEL/ATGE_2_A.CEL Wt stem, 2nd internode 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ CEL/ATGE_27_A.CEL Wt 1st node 21+ days continuous light soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ CEL/ATGE_28_A2.CEL Wt shoot apex, inflorescence (after bolting) 21 days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_29_A2.CEL Wt shoot apex, vegetative + young leaves; 7 days; AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light; soil CEL/ATGE_4_A.CEL Wt shoot apex, vegetative; 7 days; continuous light; soil AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ CEL/ATGE_6_A.CEL Wt shoot apex, transition (before bolting) 14 days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_8_A.CEL clv3-7 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_46_A.CEL lfy-12 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_47_A.CEL ap1-15 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_48_A.CEL ap2-6 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_49_A.CEL ap3-6 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_50_A.CEL ag-12 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_51_A.CEL ufo-1 shoot apex, inflorescence (after bolting) 21+ days AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ continuous light soil CEL/ATGE_52_A.CEL Root Quiescent Center; AGL42; quiescent center, Birnbaum_arexdb; non-specific pattern when roots grow old/long; QC only and at very early stages Root Phloem; APL; developing pSE and mSE and CC Birnbaum_arexdb; between the two: loss of GFP in mature pSE is accompanied by strong GFP in neighboring CC; GFP reappears in immature mSE; Root Cortex; C1 (or 315.1.1) (AT1G09750 promoter); Birnbaum_arexdb; cortex; from elongation to at least immature root hair dif. Root Epidermis; GL2; atrichoblasts; from QC and up Birnbaum_arexdb; Root Ground tissue; J0571; ground: endo + cortex + qc; Birnbaum_arexdb; from tip all the way up Lateral Root Cap; J3411; lateral root cap plus epidermis; Birnbaum_arexdb; from tip to exactly where? at least the differentiation zone; GFP is about 5X weaker in dif. zone Root Columella; PET111; columnella - tier 2,3,4; Birnbaum_arexdb; Root Xylem; S18 (477.1.3) (AT5G12870 promoter); Birnbaum_arexdb; maturing xylem cells; starts from mid-elongation and stops half way; GFP switches from pSE to mSE Root Endodermis; SCR; Marks the QC and the Birnbaum_arexdb; endodermis at least past the mature hair zone; from QC all the way up? At least past mature hair zone Tissue microdissection; Stage I; all radial tissues; Birnbaum_arexdb; where the root tip reaches its full diameter (about 0.15 mm from the root tip) Tissue microdissection; Stage II; all radial tissues; Birnbaum_arexdb; where cells transition from being optically dense to a more transparent appearance as they begin longitudinal expansion Tissue microdissection; Stage III; all radial tissues; Birnbaum_arexdb; where root hairs are fully elongated (about 0.45 to 2 mm from the root tip) Root Stele; WOL; stele; from QC and starts to fade from Birnbaum_arexdb; elongation zone Campb-Col0-Suc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A1- Campb-317.CEL Campb-Col0-noSuc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A4- Campb-320.CEL Campb-MYB61-Suc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A7- Campb-323.CEL Campb-MYB61-noSuc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A10- Campb-326.CEL Campb-MYB61oe-Suc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A13- Campb-329(new).CEL Campb-MYB61oe-noSuc Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ CEL/MC001_ATH1_A16- Campb-332.CEL col; hypocotyl Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A10.1- dubos-wth.CEL max4; hypocotyl Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A11.1- dubos-mxh.CEL axr1; hypocotyl Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A12.1- dubos-arh.CEL col; xylem Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A1.1- dubos-wtx.CEL col; cork Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A2.1- dubos-wtc.CEL myb61 ko; xylem Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A3.1- dubos-6kx.CEL myb61 ko; cork Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A4.1- dubos-6kc.CEL myb50 ko; xylem Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A5.1- dubos-5kx.CEL myb50; cork Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A6.1- dubos-5kc.CEL ler; hypocotyl Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A7.1- dubos-wLh.CEL abi1; hypocotyl (ler background) Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A8.1- dubos-aih.CEL aba1; hypocotyl (ler background) Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ CEL/MC002_ATH1_A9.1- dubos-aah.CEL seedling; Col0; 10 nM BL for 1 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA16A.cel seedling; Col0; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA17AC.cel seedling; Col0; mock treatment for 30 min AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA1AC.cel seedling; Col0; 10 nM BL for 3 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA24A.cel seedling; de-etiolated; mock treatment for 30 min AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA31A.cel seedling; de-etiolated; 10 nM BL for 30 min AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA32A.cel seedling; de-etiolated; mock treatment for 1 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA33A.cel seedling; de-etiolated; 10 nM BL for 1 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA34A.cel seedling; de-etiolated; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA35A.cel seedling; de-etiolated; 10 nM BL for 3 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA36A.cel seedling; Col0; 10 nM BL for 30 min AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA8A.cel seedling; Col0; mock treatment for 1 h AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ CEL/RIKENGODA9AC.cel complete plant; 10 uM brassinazole 91 (Brz91) AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ (brassinosteroid biosynthesis inhibitor) for 12 h CEL/RIKENGODA10A4.cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ CEL/RIKENGODA1A4.cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ CEL/RIKENGODA28A4.cel complete plant; mock treatment for 12 h AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ CEL/RIKENGODA2A4.cel complete plant; 3 uM brassinazole 220 (Brz220) AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ (brassinosteroid biosynthesis inhibitor) for 3 h CEL/RIKENGODA30A4.cel complete plant; 10 uM brassinazole 220 (Brz220) AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ (brassinosteroid biosynthesis inhibitor) for 3 h CEL/RIKENGODA7A4.cel complete plant; 10 uM paclobutrazol (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 3 h CEL/ RIKENGODA11A2.cel complete plant; 10 uM paclobutrazol (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 12 h CEL/ RIKENGODA12A2.cel complete plant; 10 uM prohexadione (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 3 h CEL/ RIKENGODA13A2.cel complete plant; 10 uM prohexadione (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 12 h CEL/ RIKENGODA14A2.cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ CEL/ RIKENGODA1A2.cel complete plant; mock treatment for 12 h AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ CEL/ RIKENGODA2A2.cel complete plant; 10 uM propiconazole (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 3 h CEL/ RIKENGODA3A2.cel complete plant; 10 uM propiconazole (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 12 h CEL/ RIKENGODA4A2.cel complete plant; 10 uM uniconazole (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 3 h CEL/ RIKENGODA5A2.cel complete plant; 10 uM uniconazole (GA biosynthesis AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ inhibitor) for 12 h CEL/ RIKENGODA6A2.cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGen_Effect_of_proteasome_inhibitor_MG13_on_seedlings/ CEL/RIKENGODA1A9. cel complete plant; 10 uM MG132 AtGenExpress; /share/nasc/AtGen_Effect_of_proteasome_inhibitor_MG13_on_seedlings/ (carbobenzoxyl-leucinyl-leucinyl-leucinal) for 3 h CEL/RIKENGODA22A9. cel seed; no treatment AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ CEL/RIKENPRESTON0A.cel seed; imbibed in water (1 hour) AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ CEL/RIKENPRESTON1A.cel seed; imbibed in water (3 hours) AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ CEL/RIKENPRESTON2A.cel seedling; 10 uM ABA for 1 h AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA13A. cel seedling; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA17A. cel seedling; mock treatment for 30 min AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA1A.cel seedling; 10 uM ABA for 3 h AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA21A. cel seedling; 10 uM ABA for 30 min AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA5A.cel seedling; mock treatment for 1 h AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA9A.cel seedling; 10 uM ACC for 1 h AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA15A. cel seedling; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA17AA. cel seedling; mock treatment for 30 min AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA1AA. cel seedling; 10 uM ACC for 3 h AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA23A. cel seedling; 10 uM ACC for 30 min AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA7A.cel seedling; mock treatment for 1 h AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ CEL/RIKENGODA9AA. cel complete plant; 10 uM 2,4,6-T (2,4,6- AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ trihydroxybenzamide) for 3 h CEL/RIKENGODA23A3. cel complete plant; 10 uM NPA (naphthylphthalamic AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ acid) (inhibitor of auxin transport) for 3 h CEL/RIKENGODA26A3. cel complete plant; 10 uM PCIB (p-chlorophenoxyisobutyric AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ acid) (auxin inhibitor) for 3 h CEL/RIKENGODA24A3. cel complete plant; 10 uM TIBA (2,3,5-triiodobenzoic acid) AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ (inhibitor of auxin transport) for 3 h CEL/RIKENGODA25A3. cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ CEL/RIKENGODA1A3.cel whole plant; 100 nM castasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA12A6. cel whole plant; 10 nM brassinolide for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA13A6. cel whole plant; 10 uM campestanol for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA2A6.cel whole plant; 1 uM 3-dehydro-6-deoxoteasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA7A6.cel whole plant; 1 uM 3-dehydroteasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA8A6.cel whole plant; 1 uM 6-deoxocastasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA11A6. cel whole plant; 1 uM 6-deoxocathasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA3A6.cel whole plant; 1 uM 6-deoxoteasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA5A6.cel whole plant; 1 uM 6-deoxotyphasterol for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA9A6.cel whole plant; 1 uM cathasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA4A6.cel whole plant; 1 uM teasterone for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA6A6.cel whole plant; 1 uM typhasterol for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA10A6. cel whole plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ CEL/RIKENGODA1A6.cel complete plant; 10 uM AgNO3 (ethylene inhibitor) AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ for 3 h CEL/RIKENGODA19A7. cel complete plant; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ CEL/RIKENGODA1A7. cel complete plant; 10 uM AVG (aminoethoxyvinylglycine) AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ (ethylene inhibitor) for 3 h CEL/RIKENGODA20A7. cel seedling; 1 uM IAA for 1 h AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA10A.cel seedling; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA17AD. cel seedling; 1 uM IAA for 3 h AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA18A.cel seedling; mock treatment for 30 min AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA1AD.cel seedling; 1 uM IAA for 30 min AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA2A.cel seedling; mock treatment for 1 h AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ CEL/RIKENGODA9AD.cel seedling; 10 uM MJ for 1 h AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA14A. cel seedling; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA17AF. cel seedling; mock treatment for 30 min AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA1AF. cel seedling; 10 uM MJ for 3 h AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA22A. cel seedling; 10 uM MJ for 30 min AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA6A. cel seedling; mock treatment for 1 h AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ CEL/RIKENGODA9AF. cel seedling; 1 uM zeatin for 1 h AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA11A. cel seedling; 1 uM zeatin for 30 min AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA3A. cel seedling; 1 uM zeatin for 3 h AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA19A. cel seedling; mock treatment for 1 h AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA9AG. cel seedling; mock treatment for 30 min AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA1AG. cel seedling; mock treatment for 3 h AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ CEL/RIKENGODA17AG. cel seeds; water treatment for 3 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI1A.cel seeds; water treatment for 6 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI2A.cel seeds; water treatment for 9 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI3A.cel seeds; 5 uM gibberellin treatment for 3 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI4A.cel seeds; 5 uM gibberellin treatment for 6 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI5A.cel seeds; 5 uM gibberellin treatment for 9 hours AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ CEL/RIKENLI6A.cel Col0; complete plant; No treatment AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ CEL/NO10.cel Col0; complete plant; 20 uM t-zeatin for 3 h AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ CEL/NO192.cel ARR22-ox; complete plant; No treatment AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ CEL/NO28.cel ARR22-ox; complete plant; 20 uM t-zeatin for 3 h AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ CEL/NO31.cel seed; 24 h imbibed in 3 uM ABA AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ CEL/RIKENNAKABAYASHI3A. cel seed; 24 h imbibed in 30 uM ABA AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ CEL/RIKENNAKABAYASHI4A. cel seed; 24 h imbibed in water AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ CEL/RIKENNAKABAYASHI2A. cel seed; no treatment AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ CEL/RIKENNAKABAYASHI1A. cel Controlstress-Shoots-0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0011.CEL Controlstress-Roots-0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0021.CEL Controlstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0111.CEL Controlstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0121.CEL Controlstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0211.CEL Controlstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0221.CEL Controlstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0311.CEL Controlstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0321.CEL Controlstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0411.CEL Controlstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0421.CEL Controlstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0511.CEL Controlstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0521.CEL Controlstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0611.CEL Controlstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0621.CEL Controlstress-Shoots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0711.CEL Controlstress-Roots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0721.CEL Controlstress-Shoots-4.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0811.CEL Controlstress-Roots-4.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ CEL/0821.CEL Coldstress(4?C)-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1111.CEL Coldstress(4?C)-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1121.CEL Coldstress(4?C)-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1211.CEL Coldstress(4?C)-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1221.CEL Coldstress(4?C)-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1311.CEL Coldstress(4?C)-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1321.CEL Coldstress(4?C)-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1411.CEL Coldstress(4?C)-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1421.CEL Coldstress(4?C)-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1511.CEL Coldstress(4?C)-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1521.CEL Coldstress(4?C)-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1611.CEL Coldstress(4?C)-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ CEL/1621.CEL Osmoticstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2111.CEL Osmoticstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2121.CEL Osmoticstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2211.CEL Osmoticstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2221.CEL Osmoticstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2311.CEL Osmoticstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2321.CEL Osmoticstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2411.CEL Osmoticstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2421.CEL Osmoticstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2511.CEL Osmoticstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2521.CEL Osmoticstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2611.CEL Osmoticstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ CEL/2621.CEL Saltstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3111.CEL Saltstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3121.CEL Saltstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3211.CEL Saltstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3221.CEL Saltstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3311.CEL Saltstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3321.CEL Saltstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3411.CEL Saltstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3421.CEL Saltstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3511.CEL Saltstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3521.CEL Saltstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3611.CEL Saltstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ CEL/3621.CEL Droughtstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4111.CEL Droughtstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4121.CEL Droughtstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4211.CEL Droughtstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4221.CEL Droughtstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4311.CEL Droughtstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4321.CEL Droughtstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4411.CEL Droughtstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4421.CEL Droughtstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4511.CEL Droughtstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4521.CEL Droughtstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4611.CEL Droughtstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4621.CEL Droughtstress-Shoots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4711.CEL Droughtstress-Roots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ CEL/4721.CEL Genotoxicstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5111.CEL Genotoxicstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5121.CEL Genotoxicstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5211.CEL Genotoxicstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5221.CEL Genotoxicstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5311.CEL Genotoxicstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5321.CEL Genotoxicstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5411.CEL Genotoxicstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5421.CEL Genotoxicstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5511.CEL Genotoxicstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5521.CEL Genotoxicstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5611.CEL Genotoxicstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ CEL/5621.CEL Oxidativestress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6111.CEL Oxidativestress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6122.CEL Oxidativestress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6211.CEL Oxidativestress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6223.CEL Oxidativestress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6311.CEL Oxidativestress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6322.CEL Oxidativestress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6411.CEL Oxidativestress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6421.CEL Oxidativestress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6511.CEL Oxidativestress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6523.CEL Oxidativestress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6611.CEL Oxidativestress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ CEL/6621.CEL UV-Bstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7111.CEL UV-Bstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7121.CEL UV-Bstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7211.CEL UV-Bstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7221.CEL UV-Bstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7311.CEL UV-Bstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7321.CEL UV-Bstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7411.CEL UV-Bstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7421.CEL UV-Bstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7511.CEL UV-Bstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7521.CEL UV-Bstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7611.CEL UV-Bstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7621.CEL UV-Bstress-Shoots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7711.CEL UV-Bstress-Roots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- B_stress/CEL/7721.CEL Woundingstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8111.CEL Woundingstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8124.CEL Woundingstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8211.CEL Woundingstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8224.CEL Woundingstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8313.CEL Woundingstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8324.CEL Woundingstress-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8411.CEL Woundingstress-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8423.CEL Woundingstress-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8511.CEL Woundingstress-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8524.CEL Woundingstress-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8611.CEL Woundingstress-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8621.CEL Woundingstress-Shoots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8712.CEL Woundingstress-Roots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ CEL/8723.CEL Heatstress-Shoots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9111.CEL Heatstress-Roots-0.5 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9121.CEL Heatstress-Shoots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9211.CEL Heatstress-Roots-1.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9221.CEL Heatstress-Shoots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9311.CEL Heatstress-Roots-3.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9321.CEL Heatstress (3 h) + 3 h recovery-Shoots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9411.CEL Heatstress (3 h) + 3 h recovery-Roots-6.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9421.CEL Heatstress (3 h) + 9 h recovery-Shoots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9511.CEL Heatstress (3 h) + 9 h recovery-Roots-12.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9521.CEL Heatstress (3 h) + 21 h recovery-Shoots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9611.CEL Heatstress (3 h) + 21 h recovery-Roots-24.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9621.CEL Heatstress-Shoots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9711.CEL Heatstress-Roots-0.25 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9721.CEL Heatstress (3 h) + 1 h recovery-Shoots-4.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9811.CEL Heatstress (3 h) + 1 h recovery-Roots-4.0 h AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ CEL/9821.CEL lateral root initiation study in xylem pole pericycle cells; in-house experiment ivsme_Col-0_NPA lateral root initiation study in xylem pole pericycle cells; in-house experiment ivsme_Col-0_2hNAA lateral root initiation study in xylem pole pericycle cells; in-house experiment ivsme_Col-0_6hNAA overexpression of two prohibitins in seedlings; in-house experiment olake_AtPHB3_overexp overexpression of two prohibitins in seedlings; in-house experiment olake_AtPHB4_overexp overexpression of two prohibitins in seedlings; in-house experiment olake_overexp_control comparison of 3 mutants (2 prohibitin, 1 auxin in-house experiment glucosyltransferase) to wild-type in seedlings; olake_knockout_AtPHB3 comparison of 3 mutants (2 prohibitin, 1 auxin in-house experiment glucosyltransferase) to wild-type in seedlings; olake_knockout_AtPHB4 comparison of 3 mutants (2 prohibitin, 1 auxin in-house experiment glucosyltransferase) to wild-type in seedlings; olake_control comparison of 3 mutants (2 prohibitin, 1 auxin in-house experiment glucosyltransferase) to wild-type in seedlings; olake_overexpression_UGTx WT landsberg erecta shoot apex seedlings compared to in-house experiment narrow leaf mutants elongata 2, 3, 4, angusta 4, drl1-2; defle_Ler WT landsberg erecta shoot apex seedlings compared to in-house experiment narrow leaf mutants elongata 2, 3, 4, angusta 4, drl1-2; defle_elo2 WT landsberg erecta shoot apex seedlings compared to in-house experiment narrow leaf mutants elongata 2, 3, 4, angusta 4, drl1-2; defle_drl1-2 WT landsberg erecta shoot apex seedlings compared to in-house experiment narrow leaf mutants elongata 2, 3, 4, angusta 4, drl1-2; defle_ang4 WT landsberg erecta shoot apex seedlings compared to in-house experiment narrow leaf mutants elongata 2, 3, 4, angusta 4, drl1-2; defle_elo3 WT shoot apex seedlings compared to narrow leaf in-house experiment mutants ELP3 (2) and SWP1 (1); defle_Ws WT shoot apex seedlings compared to narrow leaf in-house experiment mutants ELP3 (2) and SWP1 (1); defle_N3983 WT shoot apex seedlings compared to narrow leaf in-house experiment mutants ELP3 (2) and SWP1 (1); defle_219E08 WT shoot apex seedlings compared to narrow leaf in-house experiment mutants ELP3 (2) and SWP1 (1); defle_Swp1 WT landsberg erecta leaves 6 compared to broad in-house experiment leaf mutant rotunda 2; defle_ron2 WT landsberg erecta leaves 6 compared to broad in-house experiment leaf mutant rotunda 2; defle_Ler WT landsberg erecta compared to broad leaf mutant in-house experiment rotunda 1; defle_Ler WT landsberg erecta compared to broad leaf mutant in-house experiment rotunda 1; defle_ron1 WT leaves profiling at different stages of development in-house experiment (9, 15, 22 days); gebee_15 WT leaves profiling at different stages of development in-house experiment (9, 15, 22 days); gebee_22 WT leaves profiling at different stages of development in-house experiment (9, 15, 22 days); gebee_9 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-MeJA-0.5 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-MeJA-2 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-MeJA-6 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-DMSO-0.5 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-DMSO-2 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-DMSO-6 Methyl jasmonate profiling at different time points; in-house experiment lapau_ATL-MeJA-CHX-6 DEL1 knockouts versus control (columbia) in seedlings; in-house experiment livey_Wild-type_seedling_8d DEL1 knockouts versus control (columbia) in seedlings; in-house experiment livey_DEL1_KO_seedling_8d E2F overexpression versus control (columbia WT) in in-house experiment seedlings; livey_Wild-type_seedling_8d E2F overexpression versus control (columbia WT) in in-house experiment seedlings; livey_E2Fa-DPa_OE_seedling_8d DEL1 overexpression versus control (columbia WT) in in-house experiment leaf; livey_Wild-type_leaf_15d DEL1 overexpression versus control (columbia WT) in in-house experiment leaf; livey_DEL1_OE_leaf_15d endocycle exp. In leaf - control; in-house experiment livey_Wild-type_leaf_15d endocycle exp. In leaf - DEL1 knockout; in-house experiment livey_DEL1_KO_leaf_15d endocycle exp. In leaf - CCS52A1 knockout; in-house experiment livey_CCS52A1_KO_leaf_15d endocycle exp. In leaf - CCS52B knockout; in-house experiment livey_CCS52B_KO_leaf_15d endocycle exp. In leaf—CCKB1 DN; livey_CDKB1; in-house experiment 1.DN_#9_15d endocycle exp. In leaf - KRP2 overexpression; in-house experiment livey_KRP2_OE_#7_15d endocycle exp. In leaf - DEL1 overexpression; in-house experiment livey_DEL1_OE_#2_15d WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 0 h WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 0 h_HU WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 5 h WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 5 h_HU WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 1 day WEE1 exp. - genotype columbia; livey_ROOT_TIP + in-house experiment 1 day_HU WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 0 h in-house experiment WEE1 exp. - genotype WEE1; livey_ROOT_TIP + in-house experiment 0 h_HU WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 5 h in-house experiment WEE1 exp. - genotype WEE1; livey_ROOT_TIP + in-house experiment 5 h_HU WEE1 exp. - genotype WEE1; livey_ROOT_TIP + in-house experiment 1 day WEE1 exp. - genotype WEE1; livey_ROOT_TIP + in-house experiment 1 day_HU lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) WT 0 h lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) WT 2 h lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) WT 6 h lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) slr1 0 h lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) slr1 2 h lateral root initiation study WT versus mutant solitary in-house experiment root 1 (slr1) slr1 6 h vascular tissue formation - callus formed from leaves - DB001_ATH1_A3-Brown-cal.CEL 5 days after treatment; 0.2 mgl-1 auxin(2,4-D NA IAA) 1.0 mgl-1 BA vascular tissue formation - callus formed from leaves - DB001_ATH1_A4-Brown-cal.CEL 9 days after treatment; 0.2 mgl-1 auxin(2,4-D NA IAA) 1.0 mgl-1 BA Arrested development mutant analysis - leaves - add 3 BP001_ATH1_A1-Pickett-ADD3-1.CEL Arrested development mutant analysis - leaves - control BP001_ATH1_A3-Pickett-a1.CEL Agrobacterium induced tumor vs control; Tumour tissue RD001_ATH1_A1-deeke-tum.CEL induced at the base of an inflorescence stalk with Agrobacterium tumefaciens Agrobacterium induced tumor vs control; Inflorescence RD001_ATH1_A2-deeke-Inf.CEL stalk injured at the base with a injection needle (control) Polycomb binding protein knockout vs WT; WT KC001_ATH1_A1-Cain-WT1.CEL Polycomb binding protein knockout vs WT; CDB1 KC001_ATH1_A3-Cain-CDBI.CEL knockout axillary bud dormancy_naphthalene-1-acetic acid E-MEXP-148 wild-type axillary bud dormancy_max4-1 mutant E-MEXP-148 axillary bud dormancy_wild type E-MEXP-148 MPK4 on ethylene regulation E-MEXP-174 (leaf)_wild_type_Landsberg erecta MPK4 on ethylene regulation E-MEXP-174 (leaf)_ctr1 mutant_Columbia MPK4 on ethylene regulation (leaf)_mpk4 E-MEXP-174 mutant_Landsberg erecta MPK4 on ethylene regulation (leaf)_ctr1 mpk4 double E-MEXP-174 mutant_Landsberg/Columbia systemic responses of MAPK to pathogens E-MEXP-173 (leaf)_35S:mks1_eco_Landsberg systemic responses of MAPK to pathogens (leaf)_mpk4 E-MEXP-173 mutant_eco_Landsberg systemic responses of MAPK to pathogens (leaf)_wild E-MEXP-173 type_eco_Landsberg secondary cell wall E-MEXP-265 formation_hypocotyl_eco_Landsberg secondary cell wall formation_leaf_eco_Landsberg E-MEXP-265 secondary cell wall formation_stem E-MEXP-265 base_eco_Landsberg secondary cell wall formation_stem lower E-MEXP-265 middle_eco_Landsberg secondary cell wall formation_stem tip_eco_Landsberg E-MEXP-265 secondary cell wall formation_stem upper E-MEXP-265 middle_eco_Landsberg comparison of mutants lacking CAF-1 E-MEXP-694 subunits_fas2-1_eco_Landsberg erecta comparison of mutants lacking CAF-1 E-MEXP-694 subunits_msi1-as_eco_Columbia comparison of mutants lacking CAF-1 E-MEXP-694 subunits_wild_type_eco_Columbia comparison of mutants lacking CAF-1 E-MEXP-694 subunits_wild_type_eco_Enkheim comparison of mutants lacking CAF-1 E-MEXP-694 subunits_wild_type_eco_Landsberg erecta AP2/ERF TF (bolita) (leaf)_bolita mutant E-MEXP-809 AP2/ERF TF (bolita) (leaf)_wild_type E-MEXP-809 tissue comparison_stem_greenhouse Somerville: Tissue Type Arrays of Columbia-0_genome tissue comparison_leaf_greenhouse Somerville: Tissue Type Arrays of Columbia-0_genome tissue comparison_flower_growth chamber Somerville: Tissue Type Arrays of Columbia-0_genome tissue comparison_flower_greenhouse Somerville: Tissue Type Arrays of Columbia-0_genome tissue comparison_stem_growth chamber Somerville: Tissue Type Arrays of Columbia-0_genome flower_wild-type Columbia_0 days Weigel: Floral transition and early flower development flower_wild-type Columbia_3 days Weigel: Floral transition and early flower development flower_wild-type Columbia_7 days Weigel: Floral transition and early flower development flower_wild-type Landsberg_0 days Weigel: Floral transition and early flower development flower_wild-type Landsberg_3 days Weigel: Floral transition and early flower development flower_wild-type Landsberg_5 days Weigel: Floral transition and early flower development flower_wild-type Landsberg_7 days Weigel: Floral transition and early flower development flower_mutant constans (co-2)_0 days Weigel: Floral transition and early flower development flower_mutant constans (co-2)_3 days Weigel: Floral transition and early flower development flower_mutant constans (co-2)_5 days Weigel: Floral transition and early flower development flower_mutant constans (co-2)_7 days Weigel: Floral transition and early flower development flower_mutant ft (ft-2)_0 days Weigel: Floral transition and early flower development flower_mutant ft (ft-2)_3 days Weigel: Floral transition and early flower development flower_mutant ft (ft-2)_5 days Weigel: Floral transition and early flower development flower_mutant ft (ft-2)_7 days Weigel: Floral transition and early flower development flower_mutant lfy-12 Columbia_0 days Weigel: Floral transition and early flower development flower_mutant lfy-12 Columbia_3 days Weigel: Floral transition and early flower development flower_mutant lfy-12 Columbia_5 days Weigel: Floral transition and early flower development flower_mutant lfy-12 Columbia_7 days Weigel: Floral transition and early flower development laser-capture micro-dissected_embryo cotyledon (apical) /share/nasc/Casson_laser-capture_micro- dissected_embryonic_tissues/ CEL/KL001_ATH1_A1-Linds-cot.CEL laser-capture micro-dissected_embryo root (basal) /share/nasc/Casson_laser-capture_micro- dissected_embryonic_tissues/ CEL/KL001_ATH1_A1-Linds-roo.CEL laser-capture micro-dissected_globular embryo, /share/nasc/Casson_laser-capture_micro- apical tissue dissected_embryonic_tissues/ CEL/SC001_ATH1_A1.1-casso-gla. CEL laser-capture micro-dissected_globular embryo, /share/nasc/Casson_laser-capture_micro- basal tissue dissected_embryonic_tissues/ CEL/SC001_ATH1_A2.1-casso-glb. CEL laser-capture micro-dissected_heart stage embryo, /share/nasc/Casson_laser-capture_micro- cotyledon pole (apical) dissected_embryonic_tissues/ CEL/SC001_ATH1_A3-1-casso-hec. CEL laser-capture micro-dissected_heart stage embryo, /share/nasc/Casson_laser-capture_micro- root pole (basal) dissected_embryonic_tissues/ CEL/SC001_ATH1_A4-1-casso-her. CEL water-Col0-1 hr /share/nasc/De_Grauwe/CEL/DV001_ATH1_A2- degra-Cc1.CEL water-etr1 (ethylene-insensitive mutant)-1 hr /share/nasc/De_Grauwe/CEL/DV001_ATH1_A7- degra-Ec1.CEL GA4-Col0-1 hr /share/nasc/De_Grauwe/CEL/DV001_ATH1_A4- degra-Cg1.CEL GA4-etr1 (ethylene-insensitive mutant)-1 hr /share/nasc/De_Grauwe/CEL/DV001_ATH1_A9- degra-Eg1.CEL ms1ttg-young /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW001_ATH1_A1-Wilson-mla. CEL ms1ttg-old /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW002_ATH1_A2_Wilson_Rep2. CEL Ler-young /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW002_ATH1_A3_Wilson_Rep2. CEL Ler-old /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW001_ATH1_A4-Wilson-Ler. CEL Lerttg-young /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW003_ATH1_C1-GVB_rep1. CEL Lerttg-old /share/nasc/Gema_Vizcay_Barrena/ CEL/ZW003_ATH1_C2-GVB_rep1. CEL Programmed Cell Death Control /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1_Control(3)new. CEL Programmed Cell Death Heat /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1- Heat(4).CEL Programmed Cell Death Senescence /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1_Sen(3)new. CEL Wheeler-a05_SLD_SPH1 RNAi at stage 1.05, leaf /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- Wheel-a05.CEL Wheeler-a14_SLD_SPH1 RNAi at stage 1.14, leaf /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- Wheel-a14.CEL Wheeler-w05_SLD_wild type at stage 1.05, leaf /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- Wheel-w05.CEL Wheeler-w14_SLD_wild type at stage 1.14, leaf /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- Wheel-w14.CEL Ulm_1-1_4 days-345 nm /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ CEL/Ulm_1-1_4days-345nm_Rep1_ATH1. CEL Ulm_1-4_4 days-305 nm /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ CEL/Ulm_1-4_4days-305m,_Rep1_ATH1. CEL Ulm_1-9_4 days-345 nm, 1 hr-305 nm /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ CEL/Ulm_1-9_4days-345nm, 1hr- 305nm_Rep3_ATH1.CEL Ulm_1-10_4 days-345 nm, 6 hr-305 nm /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ CEL/Ulm_1-10_4days- 345nm,6hr-305nm_Rep1_ATH1.CEL microgametogenesisPollen_bicellular pollen /share/nasc/David_Honys/CEL/DH001_ATH1_A2- BCP1.CEL microgametogenesisPollen_tricellular pollen /share/nasc/David_Honys/CEL/DH001_ATH1_A3- TCP1.CEL microgametogenesisPollen_uninucleate microspores /share/nasc/David_Honys/CEL/DH001_ATH1_A1- UNM1.CEL Pourtau_1-1_lowN_leaf senescence /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ CEL/Pourtau_1- 1_lowN_Rep1_ATH1.CEL Pourtau_1-4_lowN-glu_leaf senescence_effect /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ of glucose CEL/Pourtau_1- 4_lowN-glu_Rep1_ATH1.CEL Pourtau_1-7_highN-glu_leaf senescence_effect /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ of nitrogen CEL/Pourtau_1- 7_highN-glu_Rep1_ATH1.CEL ozone-fumigated seedlings /share/nasc/Short_Functional_Genomics_of_Ozone_Stress_in_Arabidopsis/ CEL/ES001_ATH1_A1-mcain-ozo. CEL air-fumigated seedlings /share/nasc/Short_Functional_Genomics_of_Ozone_Stress_in_Arabidopsis/ CEL/ES001_ATH1_A2-mcain-con. CEL

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1. A method of isolating cell-cycle related proteins, the method comprising; performing a tap analysis using utilizing a known cell cycle protein as bait to produce results, correcting the results for non-specific interactions to produce corrected results, and reconfirming the corrected results.
 2. A method of modulating plant growth, the method comprising: identifying a cell-cycle related protein with the method of claim 1, utilizing the identified cell-cycle related protein to modulate plant growth.
 3. The method according to claim 2, wherein said cell-cycle related protein is selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790, At4g38900, At3g49240, At5g24690, At1g06070, At4g34150, At1g20480, At5g20920, At3g15970, At5g13030, At1g01880, At5g07310, At2g46610, At1g10690, At3g04710, At3g24690, At4g16130, At2g05830, At1g29220, At1g55890, At1g60650, At1g70830, At2g43140, At1g77180, At5g18620, At5g02530, At5g14170, At1g52730, At2g33340, At1g03060, At3g62240, At4g38740, At5g61220, At3g53880, At3g56860, At1g01970, At1g19520, At1g14620, At2g03820, At3g01280, At3g56690, At5g41190, At5g03740, At1g42440, At2g28450, At1g09760, At1g10840, At3g11830, At5g54900, At1g31760, At1g61870, At3g11760, At1g05805, At1g29200, At4g13850, At4g38780, At1g71380, At3g13640, At5g25060, At1g43700, At2g46020, At3g55760, At5g21160, and a variant of any thereof.
 4. A method of promoting plant growth, the method comprising utilizing a protein selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790, or a variant thereof, to promote plant growth.
 5. The method according to claim 4, wherein said utilizing is overexpression.
 6. The method according to claim 4, wherein promotion of plant growth is measured as plant biomass increase.
 7. The method according to claim 2, wherein said plant is a crop plant.
 8. The method according to claim 7, wherein said crop plant is a cereal.
 9. The method according to claim 8, wherein said cereal is selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.
 10. A cell cycle related protein isolated with the method of claim
 1. 11. The method according to claim 5, wherein promotion of plant growth is measured as plant biomass increase.
 12. The method according to claim 3, wherein the plant is a crop plant.
 13. The method according to claim 12, wherein the crop plant is a cereal.
 14. The method according to claim 13, wherein the cereal is selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.
 15. The method according to claim 4, wherein the plant is a crop plant.
 16. The method according to claim 5, wherein the plant is a crop plant.
 17. The method according to claim 6, wherein the plant is a crop plant.
 18. The method according to claim 17, wherein the crop plant is a cereal.
 19. The method according to claim 18, wherein the cereal is selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.
 20. A method of promoting growth of a plant, wherein the plant is selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum, and oat, the method comprising: overexpressing a protein in the plant, said plant selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, and At5g60790, so as to promote the plant's growth. 